Note
Go to the end to download the full example code.
Image-based meta-analysis algorithms
A tour of IBMA algorithms in NiMARE.
This tutorial is intended to provide a brief description and example of each of the IBMA algorithms implemented in NiMARE. For a more detailed introduction to the elements of an image-based meta-analysis, see other stuff.
from nilearn.plotting import plot_stat_map
Download data
Note
The data used in this example come from a collection of NIDM-Results packs downloaded from Neurovault collection 1425, uploaded by Dr. Camille Maumet.
from nimare.extract import download_nidm_pain
dset_dir = download_nidm_pain()
Load Dataset
import os
from pprint import pprint
from nimare.dataset import Dataset
from nimare.transforms import ImageTransformer
from nimare.utils import get_resource_path
dset_file = os.path.join(get_resource_path(), "nidm_pain_dset.json")
dset = Dataset(dset_file)
dset.update_path(dset_dir)
# Calculate missing images
xformer = ImageTransformer(target=["varcope", "z"])
dset = xformer.transform(dset)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning: imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.
warnings.warn(
[NiftiMasker.wrapped] Resampling images
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning: imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.
warnings.warn(
[NiftiMasker.wrapped] Resampling images
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning: imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.
warnings.warn(
[NiftiMasker.wrapped] Resampling images
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning: imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.
warnings.warn(
[NiftiMasker.wrapped] Resampling images
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning: imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.
warnings.warn(
[NiftiMasker.wrapped] Resampling images
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning: imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.
warnings.warn(
[NiftiMasker.wrapped] Resampling images
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning: imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.
warnings.warn(
[NiftiMasker.wrapped] Resampling images
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning: imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.
warnings.warn(
[NiftiMasker.wrapped] Resampling images
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning: imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.
warnings.warn(
[NiftiMasker.wrapped] Resampling images
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning: imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.
warnings.warn(
[NiftiMasker.wrapped] Resampling images
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning: imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.
warnings.warn(
[NiftiMasker.wrapped] Resampling images
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning: imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.
warnings.warn(
[NiftiMasker.wrapped] Resampling images
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning: imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.
warnings.warn(
[NiftiMasker.wrapped] Resampling images
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning: imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.
warnings.warn(
[NiftiMasker.wrapped] Resampling images
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning: imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.
warnings.warn(
[NiftiMasker.wrapped] Resampling images
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning: imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.
warnings.warn(
[NiftiMasker.wrapped] Resampling images
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning: imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.
warnings.warn(
[NiftiMasker.wrapped] Resampling images
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning: imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.
warnings.warn(
[NiftiMasker.wrapped] Resampling images
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning: imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.
warnings.warn(
[NiftiMasker.wrapped] Resampling images
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning: imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.
warnings.warn(
[NiftiMasker.wrapped] Resampling images
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning: imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.
warnings.warn(
[NiftiMasker.wrapped] Resampling images
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning: imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.
warnings.warn(
[NiftiMasker.wrapped] Resampling images
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning: imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.
warnings.warn(
[NiftiMasker.wrapped] Resampling images
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning: imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.
warnings.warn(
[NiftiMasker.wrapped] Resampling images
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning: imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.
warnings.warn(
[NiftiMasker.wrapped] Resampling images
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning: imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.
warnings.warn(
[NiftiMasker.wrapped] Resampling images
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning: imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.
warnings.warn(
[NiftiMasker.wrapped] Resampling images
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning: imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.
warnings.warn(
[NiftiMasker.wrapped] Resampling images
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning: imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.
warnings.warn(
[NiftiMasker.wrapped] Resampling images
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning: imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.
warnings.warn(
[NiftiMasker.wrapped] Resampling images
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning: imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.
warnings.warn(
[NiftiMasker.wrapped] Resampling images
Stouffer’s
from nimare.meta.ibma import Stouffers
meta = Stouffers(use_sample_size=False)
results = meta.fit(dset)
plot_stat_map(
results.get_map("z"),
cut_coords=[0, 0, -8],
draw_cross=False,
cmap="RdBu_r",
symmetric_cbar=True,
)
print("Description:")
pprint(results.description_)
print("References:")
pprint(results.bibtex_)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/plotting/img_plotting.py:1416: UserWarning: Non-finite values detected. These values will be replaced with zeros.
safe_get_data(stat_map_img, ensure_finite=True),
Description:
('An image-based meta-analysis was performed with NiMARE 0.5.0 '
'(RRID:SCR_017398; \\citealt{Salo2023}) on 21 z-statistic images using the '
'Stouffer method \\citep{stouffer1949american}.')
References:
('@article{Salo2023,\n'
' doi = {10.52294/001c.87681},\n'
' url = {https://doi.org/10.52294/001c.87681},\n'
' year = {2023},\n'
' volume = {3},\n'
' pages = {1 - 32},\n'
' author = {Taylor Salo and Tal Yarkoni and Thomas E. Nichols and '
'Jean-Baptiste Poline and Murat Bilgel and Katherine L. Bottenhorn and Dorota '
'Jarecka and James D. Kent and Adam Kimbler and Dylan M. Nielson and Kendra '
'M. Oudyk and Julio A. Peraza and Alexandre Pérez and Puck C. Reeders and '
'Julio A. Yanes and Angela R. Laird},\n'
' title = {NiMARE: Neuroimaging Meta-Analysis Research Environment},\n'
' journal = {Aperture Neuro}\n'
'}\n'
'@article{stouffer1949american,\n'
' title={The american soldier: Adjustment during army life.(studies in '
'social psychology in world war ii), vol. 1},\n'
' author={Stouffer, Samuel A and Suchman, Edward A and DeVinney, Leland C '
'and Star, Shirley A and Williams Jr, Robin M},\n'
' journal={Studies in social psychology in World War II},\n'
' year={1949},\n'
' publisher={Princeton Univ. Press}\n'
'}')
Stouffer’s with weighting by sample size
meta = Stouffers(use_sample_size=True)
results = meta.fit(dset)
plot_stat_map(
results.get_map("z"),
cut_coords=[0, 0, -8],
draw_cross=False,
cmap="RdBu_r",
symmetric_cbar=True,
)
print("Description:")
pprint(results.description_)
print("References:")
pprint(results.bibtex_)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/plotting/img_plotting.py:1416: UserWarning: Non-finite values detected. These values will be replaced with zeros.
safe_get_data(stat_map_img, ensure_finite=True),
Description:
('An image-based meta-analysis was performed with NiMARE 0.5.0 '
'(RRID:SCR_017398; \\citealt{Salo2023}) on 21 z-statistic images using the '
'Stouffer method \\citep{stouffer1949american}, with studies weighted by the '
'square root of the study sample sizes, per \\cite{zaykin2011optimally}.')
References:
('@article{Salo2023,\n'
' doi = {10.52294/001c.87681},\n'
' url = {https://doi.org/10.52294/001c.87681},\n'
' year = {2023},\n'
' volume = {3},\n'
' pages = {1 - 32},\n'
' author = {Taylor Salo and Tal Yarkoni and Thomas E. Nichols and '
'Jean-Baptiste Poline and Murat Bilgel and Katherine L. Bottenhorn and Dorota '
'Jarecka and James D. Kent and Adam Kimbler and Dylan M. Nielson and Kendra '
'M. Oudyk and Julio A. Peraza and Alexandre Pérez and Puck C. Reeders and '
'Julio A. Yanes and Angela R. Laird},\n'
' title = {NiMARE: Neuroimaging Meta-Analysis Research Environment},\n'
' journal = {Aperture Neuro}\n'
'}\n'
'@article{stouffer1949american,\n'
' title={The american soldier: Adjustment during army life.(studies in '
'social psychology in world war ii), vol. 1},\n'
' author={Stouffer, Samuel A and Suchman, Edward A and DeVinney, Leland C '
'and Star, Shirley A and Williams Jr, Robin M},\n'
' journal={Studies in social psychology in World War II},\n'
' year={1949},\n'
' publisher={Princeton Univ. Press}\n'
'}\n'
'@article{zaykin2011optimally,\n'
' title={Optimally weighted Z-test is a powerful method for combining '
'probabilities in meta-analysis},\n'
' author={Zaykin, Dmitri V},\n'
' journal={Journal of evolutionary biology},\n'
' volume={24},\n'
' number={8},\n'
' pages={1836--1841},\n'
' year={2011},\n'
' publisher={Wiley Online Library},\n'
' url={https://doi.org/10.1111/j.1420-9101.2011.02297.x},\n'
' doi={10.1111/j.1420-9101.2011.02297.x}\n'
'}')
Fisher’s
from nimare.meta.ibma import Fishers
meta = Fishers()
results = meta.fit(dset)
plot_stat_map(
results.get_map("z"),
cut_coords=[0, 0, -8],
draw_cross=False,
cmap="RdBu_r",
symmetric_cbar=True,
)
print("Description:")
pprint(results.description_)
print("References:")
pprint(results.bibtex_)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/plotting/img_plotting.py:1416: UserWarning: Non-finite values detected. These values will be replaced with zeros.
safe_get_data(stat_map_img, ensure_finite=True),
Description:
('An image-based meta-analysis was performed with NiMARE 0.5.0 '
'(RRID:SCR_017398; \\citealt{Salo2023}) on 21 z-statistic images using the '
'Fisher combined probability method \\citep{fisher1946statistical}.')
References:
('@article{Salo2023,\n'
' doi = {10.52294/001c.87681},\n'
' url = {https://doi.org/10.52294/001c.87681},\n'
' year = {2023},\n'
' volume = {3},\n'
' pages = {1 - 32},\n'
' author = {Taylor Salo and Tal Yarkoni and Thomas E. Nichols and '
'Jean-Baptiste Poline and Murat Bilgel and Katherine L. Bottenhorn and Dorota '
'Jarecka and James D. Kent and Adam Kimbler and Dylan M. Nielson and Kendra '
'M. Oudyk and Julio A. Peraza and Alexandre Pérez and Puck C. Reeders and '
'Julio A. Yanes and Angela R. Laird},\n'
' title = {NiMARE: Neuroimaging Meta-Analysis Research Environment},\n'
' journal = {Aperture Neuro}\n'
'}\n'
'@article{fisher1946statistical,\n'
' title={Statistical methods for research workers.},\n'
' author={Fisher, Ronald Aylmer and others},\n'
' journal={Statistical methods for research workers.},\n'
' number={10th. ed.},\n'
' year={1946},\n'
' publisher={Oliver and Boyd}\n'
'}')
Permuted OLS
from nimare.correct import FWECorrector
from nimare.meta.ibma import PermutedOLS
meta = PermutedOLS(two_sided=True)
results = meta.fit(dset)
plot_stat_map(
results.get_map("z"),
cut_coords=[0, 0, -8],
draw_cross=False,
cmap="RdBu_r",
symmetric_cbar=True,
)
corrector = FWECorrector(method="montecarlo", n_iters=100, n_cores=1)
cresult = corrector.transform(results)
plot_stat_map(
cresult.get_map("z_level-voxel_corr-FWE_method-montecarlo"),
cut_coords=[0, 0, -8],
draw_cross=False,
cmap="RdBu_r",
symmetric_cbar=True,
)
print("Description:")
pprint(cresult.description_)
print("References:")
pprint(cresult.bibtex_)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/plotting/img_plotting.py:1416: UserWarning: Non-finite values detected. These values will be replaced with zeros.
safe_get_data(stat_map_img, ensure_finite=True),
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/plotting/img_plotting.py:1416: UserWarning: Non-finite values detected. These values will be replaced with zeros.
safe_get_data(stat_map_img, ensure_finite=True),
Description:
('An image-based meta-analysis was performed with NiMARE 0.5.0 '
"(RRID:SCR_017398; \\citealt{Salo2023}), on 21 beta images using Nilearn's "
'\\citep{10.3389/fninf.2014.00014} permuted ordinary least squares method. '
"Family-wise error rate correction was performed using Nilearn's "
'\\citep{10.3389/fninf.2014.00014} permuted OLS method, in which null '
'distributions of test statistics were estimated using the max-value '
'permutation method detailed in \\cite{freedman1983nonstochastic}. 100 '
'iterations were performed to generate the null distribution.')
References:
('@article{10.3389/fninf.2014.00014,\n'
' title={Machine learning for neuroimaging with scikit-learn},\n'
' author={Abraham, Alexandre and Pedregosa, Fabian and Eickenberg, Michael '
'and Gervais, Philippe and Mueller, Andreas and Kossaifi, Jean and Gramfort, '
'Alexandre and Thirion, Bertrand and Varoquaux, Gael},\n'
'\tjournal={Frontiers in Neuroinformatics},\n'
'\tvolume={8},\n'
'\tyear={2014},\n'
'\turl={https://www.frontiersin.org/article/10.3389/fninf.2014.00014},\n'
'\tdoi={10.3389/fninf.2014.00014},\n'
'\tissn={1662-5196}\n'
'}\n'
'@article{Salo2023,\n'
' doi = {10.52294/001c.87681},\n'
' url = {https://doi.org/10.52294/001c.87681},\n'
' year = {2023},\n'
' volume = {3},\n'
' pages = {1 - 32},\n'
' author = {Taylor Salo and Tal Yarkoni and Thomas E. Nichols and '
'Jean-Baptiste Poline and Murat Bilgel and Katherine L. Bottenhorn and Dorota '
'Jarecka and James D. Kent and Adam Kimbler and Dylan M. Nielson and Kendra '
'M. Oudyk and Julio A. Peraza and Alexandre Pérez and Puck C. Reeders and '
'Julio A. Yanes and Angela R. Laird},\n'
' title = {NiMARE: Neuroimaging Meta-Analysis Research Environment},\n'
' journal = {Aperture Neuro}\n'
'}\n'
'@article{freedman1983nonstochastic,\n'
' title={A nonstochastic interpretation of reported significance levels},\n'
' author={Freedman, David and Lane, David},\n'
' journal={Journal of Business \\& Economic Statistics},\n'
' volume={1},\n'
' number={4},\n'
' pages={292--298},\n'
' year={1983},\n'
' publisher={Taylor \\& Francis}\n'
'}')
Weighted Least Squares
from nimare.meta.ibma import WeightedLeastSquares
meta = WeightedLeastSquares(tau2=0)
results = meta.fit(dset)
plot_stat_map(
results.get_map("z"),
cut_coords=[0, 0, -8],
draw_cross=False,
cmap="RdBu_r",
symmetric_cbar=True,
)
print("Description:")
pprint(results.description_)
print("References:")
pprint(results.bibtex_)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/plotting/img_plotting.py:1416: UserWarning: Non-finite values detected. These values will be replaced with zeros.
safe_get_data(stat_map_img, ensure_finite=True),
Description:
('An image-based meta-analysis was performed with NiMARE 0.5.0 '
'(RRID:SCR_017398; \\citealt{Salo2023}), on 21 beta images using the Weighted '
'Least Squares approach \\citep{brockwell2001comparison}, with an a priori '
'tau-squared value of 0 defined across all voxels.')
References:
('@article{Salo2023,\n'
' doi = {10.52294/001c.87681},\n'
' url = {https://doi.org/10.52294/001c.87681},\n'
' year = {2023},\n'
' volume = {3},\n'
' pages = {1 - 32},\n'
' author = {Taylor Salo and Tal Yarkoni and Thomas E. Nichols and '
'Jean-Baptiste Poline and Murat Bilgel and Katherine L. Bottenhorn and Dorota '
'Jarecka and James D. Kent and Adam Kimbler and Dylan M. Nielson and Kendra '
'M. Oudyk and Julio A. Peraza and Alexandre Pérez and Puck C. Reeders and '
'Julio A. Yanes and Angela R. Laird},\n'
' title = {NiMARE: Neuroimaging Meta-Analysis Research Environment},\n'
' journal = {Aperture Neuro}\n'
'}\n'
'@article{brockwell2001comparison,\n'
' title={A comparison of statistical methods for meta-analysis},\n'
' author={Brockwell, Sarah E and Gordon, Ian R},\n'
' journal={Statistics in medicine},\n'
' volume={20},\n'
' number={6},\n'
' pages={825--840},\n'
' year={2001},\n'
' publisher={Wiley Online Library},\n'
' url={https://doi.org/10.1002/sim.650},\n'
' doi={10.1002/sim.650}\n'
'}')
DerSimonian-Laird
from nimare.meta.ibma import DerSimonianLaird
meta = DerSimonianLaird()
results = meta.fit(dset)
plot_stat_map(
results.get_map("z"),
cut_coords=[0, 0, -8],
draw_cross=False,
cmap="RdBu_r",
symmetric_cbar=True,
)
print("Description:")
pprint(results.description_)
print("References:")
pprint(results.bibtex_)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/plotting/img_plotting.py:1416: UserWarning: Non-finite values detected. These values will be replaced with zeros.
safe_get_data(stat_map_img, ensure_finite=True),
Description:
('An image-based meta-analysis was performed with NiMARE 0.5.0 '
'(RRID:SCR_017398; \\citealt{Salo2023}), on 21 beta and variance images using '
'the DerSimonian-Laird method \\citep{dersimonian1986meta}, in which '
'tau-squared is estimated on a voxel-wise basis using the method-of-moments '
'approach \\citep{dersimonian1986meta,kosmidis2017improving}.')
References:
('@article{Salo2023,\n'
' doi = {10.52294/001c.87681},\n'
' url = {https://doi.org/10.52294/001c.87681},\n'
' year = {2023},\n'
' volume = {3},\n'
' pages = {1 - 32},\n'
' author = {Taylor Salo and Tal Yarkoni and Thomas E. Nichols and '
'Jean-Baptiste Poline and Murat Bilgel and Katherine L. Bottenhorn and Dorota '
'Jarecka and James D. Kent and Adam Kimbler and Dylan M. Nielson and Kendra '
'M. Oudyk and Julio A. Peraza and Alexandre Pérez and Puck C. Reeders and '
'Julio A. Yanes and Angela R. Laird},\n'
' title = {NiMARE: Neuroimaging Meta-Analysis Research Environment},\n'
' journal = {Aperture Neuro}\n'
'}\n'
'@article{dersimonian1986meta,\n'
' title={Meta-analysis in clinical trials},\n'
' author={DerSimonian, Rebecca and Laird, Nan},\n'
' journal={Controlled clinical trials},\n'
' volume={7},\n'
' number={3},\n'
' pages={177--188},\n'
' year={1986},\n'
' publisher={Elsevier}\n'
'}\n'
'@article{kosmidis2017improving,\n'
' title={Improving the accuracy of likelihood-based inference in '
'meta-analysis and meta-regression},\n'
' author={Kosmidis, Ioannis and Guolo, Annamaria and Varin, Cristiano},\n'
' journal={Biometrika},\n'
' volume={104},\n'
' number={2},\n'
' pages={489--496},\n'
' year={2017},\n'
' publisher={Oxford University Press},\n'
' url={https://doi.org/10.1093/biomet/asx001},\n'
' doi={10.1093/biomet/asx001}\n'
'}')
Hedges
from nimare.meta.ibma import Hedges
meta = Hedges()
results = meta.fit(dset)
plot_stat_map(
results.get_map("z"),
cut_coords=[0, 0, -8],
draw_cross=False,
cmap="RdBu_r",
symmetric_cbar=True,
)
print("Description:")
pprint(results.description_)
print("References:")
pprint(results.bibtex_)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/plotting/img_plotting.py:1416: UserWarning: Non-finite values detected. These values will be replaced with zeros.
safe_get_data(stat_map_img, ensure_finite=True),
Description:
('An image-based meta-analysis was performed with NiMARE 0.5.0 '
'(RRID:SCR_017398; \\citealt{Salo2023}), on 21 beta and variance images using '
'the Hedges method \\citep{hedges2014statistical}, in which tau-squared is '
'estimated on a voxel-wise basis.')
References:
('@article{Salo2023,\n'
' doi = {10.52294/001c.87681},\n'
' url = {https://doi.org/10.52294/001c.87681},\n'
' year = {2023},\n'
' volume = {3},\n'
' pages = {1 - 32},\n'
' author = {Taylor Salo and Tal Yarkoni and Thomas E. Nichols and '
'Jean-Baptiste Poline and Murat Bilgel and Katherine L. Bottenhorn and Dorota '
'Jarecka and James D. Kent and Adam Kimbler and Dylan M. Nielson and Kendra '
'M. Oudyk and Julio A. Peraza and Alexandre Pérez and Puck C. Reeders and '
'Julio A. Yanes and Angela R. Laird},\n'
' title = {NiMARE: Neuroimaging Meta-Analysis Research Environment},\n'
' journal = {Aperture Neuro}\n'
'}\n'
'@book{hedges2014statistical,\n'
' title={Statistical methods for meta-analysis},\n'
' author={Hedges, Larry V and Olkin, Ingram},\n'
' year={2014},\n'
' publisher={Academic press}\n'
'}')
Fixed Effects Meta-Analysis with Hedges’ g
from nimare.meta.ibma import FixedEffectsHedges
meta = FixedEffectsHedges(tau2=0)
results = meta.fit(dset)
plot_stat_map(
results.get_map("z"),
cut_coords=[0, 0, -8],
draw_cross=False,
cmap="RdBu_r",
symmetric_cbar=True,
)
print("Description:")
pprint(results.description_)
print("References:")
pprint(results.bibtex_)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/checkouts/stable/nimare/meta/ibma.py:118: FutureWarning: 'force_resample' will be set to 'True' by default in Nilearn 0.13.0.
Use 'force_resample=True' to suppress this warning.
else resample_to_img(nib.load(img), mask_img, **self._resample_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/image/resampling.py:805: FutureWarning: From release 0.13.0 onwards, this function will, by default, copy the header of the input image to the output. Currently, the header is reset to the default Nifti1Header. To suppress this warning and use the new behavior, set `copy_header=True`.
return resample_img(
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/stable/lib/python3.9/site-packages/nilearn/plotting/img_plotting.py:1416: UserWarning: Non-finite values detected. These values will be replaced with zeros.
safe_get_data(stat_map_img, ensure_finite=True),
Description:
('An image-based meta-analysis was performed with NiMARE 0.5.0 '
'(RRID:SCR_017398; \\citealt{Salo2023}), on 21 t-statistic images using '
"Heges' g as point estimates and the variance of bias-corrected Cohen's in a "
'Weighted Least Squares approach '
'\\citep{brockwell2001comparison,bossier2019}, with an a priori tau-squared '
'value of 0 defined across all voxels.')
References:
('@article{Salo2023,\n'
' doi = {10.52294/001c.87681},\n'
' url = {https://doi.org/10.52294/001c.87681},\n'
' year = {2023},\n'
' volume = {3},\n'
' pages = {1 - 32},\n'
' author = {Taylor Salo and Tal Yarkoni and Thomas E. Nichols and '
'Jean-Baptiste Poline and Murat Bilgel and Katherine L. Bottenhorn and Dorota '
'Jarecka and James D. Kent and Adam Kimbler and Dylan M. Nielson and Kendra '
'M. Oudyk and Julio A. Peraza and Alexandre Pérez and Puck C. Reeders and '
'Julio A. Yanes and Angela R. Laird},\n'
' title = {NiMARE: Neuroimaging Meta-Analysis Research Environment},\n'
' journal = {Aperture Neuro}\n'
'}\n'
'@article{brockwell2001comparison,\n'
' title={A comparison of statistical methods for meta-analysis},\n'
' author={Brockwell, Sarah E and Gordon, Ian R},\n'
' journal={Statistics in medicine},\n'
' volume={20},\n'
' number={6},\n'
' pages={825--840},\n'
' year={2001},\n'
' publisher={Wiley Online Library},\n'
' url={https://doi.org/10.1002/sim.650},\n'
' doi={10.1002/sim.650}\n'
'}')
Total running time of the script: (1 minutes 7.111 seconds)