Snakebids pipeline for anatomical preprocessing with gradcorrect, 3dMPRAGEise, synthstrip, fMRIPrep and ciftify.
-
Bids dataset with:
- MP2RAGE data (uni and inv2)
- T2w (will be added soon)
-
dependencies:
- python:
- snakebids: https://github.com/akhanf/snakebids
- singularity containers:
- python:
-
Create and activate virtual environment minimum python version >= 3.7 and install snakebids version == 0.6.2
-
on Compute Canada:
module load python/3.8 virtualenv --no-download your_virtual_env_name_here source your_virtual_env_name_here/bin/activate pip install snakebids==0.6.2
-
-
Change directory to
anat_preproc/anat_preproc(to be in same directory asrun.pyfile).cd anat_preproc/anat_preproc
-
Use below listed run options to run pipeline.
-
Skipping gradient distortion correction:
python run.py bids_dir out_dir participant -
running gradient correction:
python run.py bids_dir out_dir participant --grad_coef your_grad_coef_file.grad -
on Compute Canada you can use https://github.com/khanlab/cc-slurm to submit jobs with SLURM.
python run.py bids_dir out_dir participant --grad_coef your_grad_coef_file.grad --profile cc-slurm -
NOTE: you are likely going to have to specify inv2 and uni file paths with wildcards in your command given your dataset specific naming conventions.
- example:
python run.py \ /scratch/myousif9/snsx_inprogress/sourcedata/SNSX_7T/tar2bids_v0.0.5e/bids/ /scratch/myousif9/snsx_inprogress/output/anat_preproc_gradient_corr_test participant \ --path-uni /scratch/myousif9/snsx_inprogress/sourcedata/SNSX_7T/tar2bids_v0.0.5e/bids/sub-{subject}/anat/sub-{subject}_acq-UNI_run-01_MP2RAGE.nii.gz \ --path-inv2 /scratch/myousif9/snsx_inprogress/sourcedata/SNSX_7T/tar2bids_v0.0.5e/bids/sub-{subject}/anat/sub-{subject}_inv-2_run-01_MP2RAGE.nii.gz \ --participant_label C001 \ --grad_coef /project/ctb-akhanf/myousif9/gradcorrect_ref_file/coeff_AC84.grad \ --profile cc-slurm
- example:
-
(snakemake) [myousif9@gra-login2 anat_preproc]$ python run.py -h
usage: run.py [-h] [--pybidsdb-dir PYBIDSDB_DIR] [--reset-db] [--force-output]
[--help-snakemake]
[--participant-label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
[--exclude_participant_label EXCLUDE_PARTICIPANT_LABEL [EXCLUDE_PARTICIPANT_LABEL ...]]
[--derivatives DERIVATIVES [DERIVATIVES ...]]
[--fs_license FS_LICENSE] [--grad_coef GRAD_COEF]
[--filter-uni FILTER_UNI [FILTER_UNI ...]]
[--filter-inv2 FILTER_INV2 [FILTER_INV2 ...]]
[--wildcards-uni WILDCARDS_UNI [WILDCARDS_UNI ...]]
[--wildcards-inv2 WILDCARDS_INV2 [WILDCARDS_INV2 ...]]
[--path-uni PATH_UNI] [--path-inv2 PATH_INV2]
bids_dir output_dir {participant}
Snakebids helps build BIDS Apps with Snakemake
optional arguments:
-h, --help show this help message and exit
STANDARD:
Standard options for all snakebids apps
--pybidsdb-dir PYBIDSDB_DIR, --pybidsdb_dir PYBIDSDB_DIR
Optional path to directory of SQLite databasefile for
PyBIDS. If directory is passed and folder exists,
indexing is skipped. If reset_db is called, indexing
will persist
--reset-db, --reset_db
Reindex existing PyBIDS SQLite database
--force-output, --force_output
Force output in a new directory that already has
contents
--help-snakemake, --help_snakemake
Options to Snakemake can also be passed directly at
the command-line, use this to print Snakemake usage
SNAKEBIDS:
Options for snakebids app
bids_dir The directory with the input dataset formatted
according to the BIDS standard.
output_dir The directory where the output files should be stored.
If you are running group level analysis this folder
should be prepopulated with the results of the
participant level analysis.
{participant} Level of the analysis that will be performed.
--participant-label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...], --participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
The label(s) of the participant(s) that should be
analyzed. The label corresponds to
sub-<participant_label> from the BIDS spec (so it does
not include "sub-"). If this parameter is not provided
all subjects should be analyzed. Multiple participants
can be specified with a space separated list.
--exclude_participant_label EXCLUDE_PARTICIPANT_LABEL [EXCLUDE_PARTICIPANT_LABEL ...], --exclude-participant-label EXCLUDE_PARTICIPANT_LABEL [EXCLUDE_PARTICIPANT_LABEL ...]
The label(s) of the participant(s) that should be
excluded. The label corresponds to
sub-<participant_label> from the BIDS spec (so it does
not include "sub-"). If this parameter is not provided
all subjects should be analyzed. Multiple participants
can be specified with a space separated list.
--derivatives DERIVATIVES [DERIVATIVES ...]
Path(s) to a derivatives dataset, for folder(s) that
contains multiple derivatives datasets (default:
False)
--fs_license FS_LICENSE, --fs-license FS_LICENSE
Provide path to freesurfer license text file.
--grad_coef GRAD_COEF, --grad-coef GRAD_COEF
Provide path to gradient correction coefficient file.
Gradient correction dis skipped if file is not
specified.
BIDS FILTERS:
Filters to customize PyBIDS get() as key=value pairs
--filter-uni FILTER_UNI [FILTER_UNI ...], --filter_uni FILTER_UNI [FILTER_UNI ...]
(default: suffix=MP2RAGE extension=.nii.gz
datatype=anat acquisition=UNI invalid_filters=allow
echo=None)
--filter-inv2 FILTER_INV2 [FILTER_INV2 ...], --filter_inv2 FILTER_INV2 [FILTER_INV2 ...]
(default: suffix=MP2RAGE extension=.nii.gz
datatype=anat inv=2 invalid_filters=allow echo=None)
INPUT WILDCARDS:
File path entities to use as wildcards in snakemake
--wildcards-uni WILDCARDS_UNI [WILDCARDS_UNI ...], --wildcards_uni WILDCARDS_UNI [WILDCARDS_UNI ...]
(default: subject session acquisition task run)
--wildcards-inv2 WILDCARDS_INV2 [WILDCARDS_INV2 ...], --wildcards_inv2 WILDCARDS_INV2 [WILDCARDS_INV2 ...]
(default: subject session acquisition task run)
PATH OVERRIDE:
Options for overriding BIDS by specifying absolute paths that include
wildcards, e.g.: /path/to/my_data/{subject}/t1.nii.gz
--path-uni PATH_UNI, --path_uni PATH_UNI
--path-inv2 PATH_INV2, --path_inv2 PATH_INV2
anat_preproc_gradient_corr_test/
├── config
├── derivatives
│ ├── 3dmprageise
│ ├── ciftify
│ ├── fmriprep
│ ├── gradcorrect
│ └── synthstrip
├── logs
│ ├── slurm
│ └── sub-C001
└── work
├── fmriprep
└── sub-C001
derivatives/
├── 3dmprageise
│ └── sub-C001
│ └── anat
│ └── sub-C001_desc-mprageise_T1w.nii.gz
├── ciftify
│ ├── qc_recon_all
│ │ ├── aseg_Ax.html
│ │ ├── aseg_Cor.html
│ │ ├── aseg_Sag.html
│ │ ├── index.html
│ │ ├── MNI_LM.html
│ │ ├── MNI_LRDV.html
│ │ ├── MNI_surf_Ax.html
│ │ ├── MNI_surf_Cor.html
│ │ ├── MNI_surf_Sag.html
│ │ └── sub-C001
│ │ ├── aparc.png
│ │ ├── aseg_Ax.png
│ │ ├── aseg_Cor.png
│ │ ├── aseg_Sag.png
│ │ ├── curv.png
│ │ ├── MNI_LM.png
│ │ ├── MNI_LRDV.png
│ │ ├── MNI_surf_Ax.png
│ │ ├── MNI_surf_Cor.png
│ │ ├── MNI_surf_Sag.png
│ │ ├── native_LRDV.png
│ │ ├── native_surf_Ax.png
│ │ ├── native_surf_Cor.png
│ │ ├── native_surf_Sag.png
│ │ ├── qc.html
│ │ └── thickness.png
│ ├── sub-C001
│ │ ├── cifti_recon_all.log
│ │ ├── MNINonLinear
│ │ │ ├── aparc.a2009s+aseg.nii.gz
│ │ │ ├── aparc+aseg.nii.gz
│ │ │ ├── brainmask_fs.nii.gz
│ │ │ ├── fsaverage_LR32k
│ │ │ │ ├── sub-C001.32k_fs_LR.wb.spec
│ │ │ │ ├── sub-C001.aparc.32k_fs_LR.dlabel.nii
│ │ │ │ ├── sub-C001.aparc.a2009s.32k_fs_LR.dlabel.nii
│ │ │ │ ├── sub-C001.aparc.DKTatlas.32k_fs_LR.dlabel.nii
│ │ │ │ ├── sub-C001.ArealDistortion_FS.32k_fs_LR.dscalar.nii
│ │ │ │ ├── sub-C001.ArealDistortion_MSMSulc.32k_fs_LR.dscalar.nii
│ │ │ │ ├── sub-C001.BA_exvivo.32k_fs_LR.dlabel.nii
│ │ │ │ ├── sub-C001.curvature.32k_fs_LR.dscalar.nii
│ │ │ │ ├── sub-C001.EdgeDistortion_MSMSulc.32k_fs_LR.dscalar.nii
│ │ │ │ ├── sub-C001.L.atlasroi.32k_fs_LR.shape.gii
│ │ │ │ ├── sub-C001.L.flat.32k_fs_LR.surf.gii
│ │ │ │ ├── sub-C001.L.inflated.32k_fs_LR.surf.gii
│ │ │ │ ├── sub-C001.L.midthickness.32k_fs_LR.surf.gii
│ │ │ │ ├── sub-C001.L.pial.32k_fs_LR.surf.gii
│ │ │ │ ├── sub-C001.L.sphere.32k_fs_LR.surf.gii
│ │ │ │ ├── sub-C001.L.very_inflated.32k_fs_LR.surf.gii
│ │ │ │ ├── sub-C001.L.white.32k_fs_LR.surf.gii
│ │ │ │ ├── sub-C001.R.atlasroi.32k_fs_LR.shape.gii
│ │ │ │ ├── sub-C001.R.flat.32k_fs_LR.surf.gii
│ │ │ │ ├── sub-C001.R.inflated.32k_fs_LR.surf.gii
│ │ │ │ ├── sub-C001.R.midthickness.32k_fs_LR.surf.gii
│ │ │ │ ├── sub-C001.R.pial.32k_fs_LR.surf.gii
│ │ │ │ ├── sub-C001.R.sphere.32k_fs_LR.surf.gii
│ │ │ │ ├── sub-C001.R.very_inflated.32k_fs_LR.surf.gii
│ │ │ │ ├── sub-C001.R.white.32k_fs_LR.surf.gii
│ │ │ │ ├── sub-C001.sulc.32k_fs_LR.dscalar.nii
│ │ │ │ └── sub-C001.thickness.32k_fs_LR.dscalar.nii
│ │ │ ├── Native
│ │ │ │ ├── MSMSulc
│ │ │ │ ├── sub-C001.aparc.a2009s.native.dlabel.nii
│ │ │ │ ├── sub-C001.aparc.DKTatlas.native.dlabel.nii
│ │ │ │ ├── sub-C001.aparc.native.dlabel.nii
│ │ │ │ ├── sub-C001.ArealDistortion_FS.native.dscalar.nii
│ │ │ │ ├── sub-C001.ArealDistortion_MSMSulc.native.dscalar.nii
│ │ │ │ ├── sub-C001.BA_exvivo.native.dlabel.nii
│ │ │ │ ├── sub-C001.curvature.native.dscalar.nii
│ │ │ │ ├── sub-C001.EdgeDistortion_MSMSulc.native.dscalar.nii
│ │ │ │ ├── sub-C001.L.inflated.native.surf.gii
│ │ │ │ ├── sub-C001.L.midthickness.native.surf.gii
│ │ │ │ ├── sub-C001.L.pial.native.surf.gii
│ │ │ │ ├── sub-C001.L.roi.native.shape.gii
│ │ │ │ ├── sub-C001.L.sphere.MSMSulc.native.surf.gii
│ │ │ │ ├── sub-C001.L.sphere.native.surf.gii
│ │ │ │ ├── sub-C001.L.sphere.reg.native.surf.gii
│ │ │ │ ├── sub-C001.L.sphere.reg.reg_LR.native.surf.gii
│ │ │ │ ├── sub-C001.L.sphere.rot.native.surf.gii
│ │ │ │ ├── sub-C001.L.very_inflated.native.surf.gii
│ │ │ │ ├── sub-C001.L.white.native.surf.gii
│ │ │ │ ├── sub-C001.native.wb.spec
│ │ │ │ ├── sub-C001.R.inflated.native.surf.gii
│ │ │ │ ├── sub-C001.R.midthickness.native.surf.gii
│ │ │ │ ├── sub-C001.R.pial.native.surf.gii
│ │ │ │ ├── sub-C001.R.roi.native.shape.gii
│ │ │ │ ├── sub-C001.R.sphere.MSMSulc.native.surf.gii
│ │ │ │ ├── sub-C001.R.sphere.native.surf.gii
│ │ │ │ ├── sub-C001.R.sphere.reg.native.surf.gii
│ │ │ │ ├── sub-C001.R.sphere.reg.reg_LR.native.surf.gii
│ │ │ │ ├── sub-C001.R.sphere.rot.native.surf.gii
│ │ │ │ ├── sub-C001.R.very_inflated.native.surf.gii
│ │ │ │ ├── sub-C001.R.white.native.surf.gii
│ │ │ │ ├── sub-C001.sulc.native.dscalar.nii
│ │ │ │ └── sub-C001.thickness.native.dscalar.nii
│ │ │ ├── Results
│ │ │ ├── ROIs
│ │ │ │ ├── Atlas_ROIs.2.nii.gz
│ │ │ │ └── ROIs.2.nii.gz
│ │ │ ├── sub-C001.164k_fs_LR.wb.spec
│ │ │ ├── sub-C001.aparc.164k_fs_LR.dlabel.nii
│ │ │ ├── sub-C001.aparc.a2009s.164k_fs_LR.dlabel.nii
│ │ │ ├── sub-C001.aparc.DKTatlas.164k_fs_LR.dlabel.nii
│ │ │ ├── sub-C001.ArealDistortion_FS.164k_fs_LR.dscalar.nii
│ │ │ ├── sub-C001.ArealDistortion_MSMSulc.164k_fs_LR.dscalar.nii
│ │ │ ├── sub-C001.BA_exvivo.164k_fs_LR.dlabel.nii
│ │ │ ├── sub-C001.curvature.164k_fs_LR.dscalar.nii
│ │ │ ├── sub-C001.EdgeDistortion_MSMSulc.164k_fs_LR.dscalar.nii
│ │ │ ├── sub-C001.L.atlasroi.164k_fs_LR.shape.gii
│ │ │ ├── sub-C001.L.flat.164k_fs_LR.surf.gii
│ │ │ ├── sub-C001.L.inflated.164k_fs_LR.surf.gii
│ │ │ ├── sub-C001.L.midthickness.164k_fs_LR.surf.gii
│ │ │ ├── sub-C001.L.pial.164k_fs_LR.surf.gii
│ │ │ ├── sub-C001.L.sphere.164k_fs_LR.surf.gii
│ │ │ ├── sub-C001.L.very_inflated.164k_fs_LR.surf.gii
│ │ │ ├── sub-C001.L.white.164k_fs_LR.surf.gii
│ │ │ ├── sub-C001.R.atlasroi.164k_fs_LR.shape.gii
│ │ │ ├── sub-C001.R.flat.164k_fs_LR.surf.gii
│ │ │ ├── sub-C001.R.inflated.164k_fs_LR.surf.gii
│ │ │ ├── sub-C001.R.midthickness.164k_fs_LR.surf.gii
│ │ │ ├── sub-C001.R.pial.164k_fs_LR.surf.gii
│ │ │ ├── sub-C001.R.sphere.164k_fs_LR.surf.gii
│ │ │ ├── sub-C001.R.very_inflated.164k_fs_LR.surf.gii
│ │ │ ├── sub-C001.R.white.164k_fs_LR.surf.gii
│ │ │ ├── sub-C001.sulc.164k_fs_LR.dscalar.nii
│ │ │ ├── sub-C001.thickness.164k_fs_LR.dscalar.nii
│ │ │ ├── T1w.nii.gz
│ │ │ ├── wmparc.nii.gz
│ │ │ └── xfms
│ │ │ ├── NonlinearReg_fromlinear.log
│ │ │ ├── Standard2T1w_warp_noaffine.nii.gz
│ │ │ ├── T1w2StandardLinear.mat
│ │ │ └── T1w2Standard_warp_noaffine.nii.gz
│ │ └── T1w
│ │ ├── aparc.a2009s+aseg.nii.gz
│ │ ├── aparc+aseg.nii.gz
│ │ ├── brainmask_fs.nii.gz
│ │ ├── fsaverage_LR32k
│ │ │ ├── sub-C001.32k_fs_LR.wb.spec
│ │ │ ├── sub-C001.L.inflated.32k_fs_LR.surf.gii
│ │ │ ├── sub-C001.L.midthickness.32k_fs_LR.surf.gii
│ │ │ ├── sub-C001.L.pial.32k_fs_LR.surf.gii
│ │ │ ├── sub-C001.L.sphere.32k_fs_LR.surf.gii
│ │ │ ├── sub-C001.L.very_inflated.32k_fs_LR.surf.gii
│ │ │ ├── sub-C001.L.white.32k_fs_LR.surf.gii
│ │ │ ├── sub-C001.R.inflated.32k_fs_LR.surf.gii
│ │ │ ├── sub-C001.R.midthickness.32k_fs_LR.surf.gii
│ │ │ ├── sub-C001.R.pial.32k_fs_LR.surf.gii
│ │ │ ├── sub-C001.R.sphere.32k_fs_LR.surf.gii
│ │ │ ├── sub-C001.R.very_inflated.32k_fs_LR.surf.gii
│ │ │ └── sub-C001.R.white.32k_fs_LR.surf.gii
│ │ ├── Native
│ │ │ ├── sub-C001.L.inflated.native.surf.gii
│ │ │ ├── sub-C001.L.midthickness.native.surf.gii
│ │ │ ├── sub-C001.L.pial.native.surf.gii
│ │ │ ├── sub-C001.L.very_inflated.native.surf.gii
│ │ │ ├── sub-C001.L.white.native.surf.gii
│ │ │ ├── sub-C001.native.wb.spec
│ │ │ ├── sub-C001.R.inflated.native.surf.gii
│ │ │ ├── sub-C001.R.midthickness.native.surf.gii
│ │ │ ├── sub-C001.R.pial.native.surf.gii
│ │ │ ├── sub-C001.R.very_inflated.native.surf.gii
│ │ │ └── sub-C001.R.white.native.surf.gii
│ │ ├── T1w_brain.nii.gz
│ │ ├── T1w.nii.gz
│ │ └── wmparc.nii.gz
│ └── zz_templates
│ ├── Atlas_ROIs.2.nii.gz
│ ├── colin.cerebral.L.flat.164k_fs_LR.surf.gii
│ ├── colin.cerebral.L.flat.32k_fs_LR.surf.gii
│ ├── colin.cerebral.R.flat.164k_fs_LR.surf.gii
│ ├── colin.cerebral.R.flat.32k_fs_LR.surf.gii
│ ├── fsaverage.L_LR.spherical_std.164k_fs_LR.surf.gii
│ ├── fsaverage.R_LR.spherical_std.164k_fs_LR.surf.gii
│ ├── L.atlasroi.164k_fs_LR.shape.gii
│ ├── L.atlasroi.32k_fs_LR.shape.gii
│ ├── L.sphere.32k_fs_LR.surf.gii
│ ├── R.atlasroi.164k_fs_LR.shape.gii
│ ├── R.atlasroi.32k_fs_LR.shape.gii
│ └── R.sphere.32k_fs_LR.surf.gii
├── fmriprep
│ ├── dataset_description.json
│ ├── desc-aparcaseg_dseg.tsv
│ ├── desc-aseg_dseg.tsv
│ ├── logs
│ │ ├── CITATION.bib
│ │ ├── CITATION.html
│ │ ├── CITATION.md
│ │ └── CITATION.tex
│ ├── sourcedata
│ │ └── freesurfer
│ │ ├── fsaverage
│ │ │ ├── label
│ │ │ ├── mri
│ │ │ ├── mri.2mm
│ │ │ ├── scripts
│ │ │ ├── surf
│ │ │ └── xhemi
│ │ └── sub-C001
│ │ ├── label
│ │ ├── mri
│ │ ├── scripts
│ │ ├── stats
│ │ ├── surf
│ │ ├── tmp
│ │ ├── touch
│ │ └── trash
│ ├── sub-C001
│ │ ├── anat
│ │ │ ├── sub-C001_desc-aparcaseg_dseg.nii.gz
│ │ │ ├── sub-C001_desc-aseg_dseg.nii.gz
│ │ │ ├── sub-C001_desc-brain_mask.json
│ │ │ ├── sub-C001_desc-brain_mask.nii.gz
│ │ │ ├── sub-C001_desc-preproc_T1w.json
│ │ │ ├── sub-C001_desc-preproc_T1w.nii.gz
│ │ │ ├── sub-C001_desc-synthstrip_dseg.nii.gz
│ │ │ ├── sub-C001_from-fsnative_to-T1w_mode-image_xfm.txt
│ │ │ ├── sub-C001_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
│ │ │ ├── sub-C001_from-T1w_to-fsnative_mode-image_xfm.txt
│ │ │ ├── sub-C001_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
│ │ │ ├── sub-C001_hemi-L_inflated.surf.gii
│ │ │ ├── sub-C001_hemi-L_midthickness.surf.gii
│ │ │ ├── sub-C001_hemi-L_pial.surf.gii
│ │ │ ├── sub-C001_hemi-L_smoothwm.surf.gii
│ │ │ ├── sub-C001_hemi-R_inflated.surf.gii
│ │ │ ├── sub-C001_hemi-R_midthickness.surf.gii
│ │ │ ├── sub-C001_hemi-R_pial.surf.gii
│ │ │ ├── sub-C001_hemi-R_smoothwm.surf.gii
│ │ │ ├── sub-C001_label-CSF_desc-synthstrip_probseg.nii.gz
│ │ │ ├── sub-C001_label-GM_desc-synthstrip_probseg.nii.gz
│ │ │ ├── sub-C001_label-WM_desc-synthstrip_probseg.nii.gz
│ │ │ ├── sub-C001_space-MNI152NLin2009cAsym_desc-brain_mask.json
│ │ │ ├── sub-C001_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
│ │ │ ├── sub-C001_space-MNI152NLin2009cAsym_desc-preproc_T1w.json
│ │ │ ├── sub-C001_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
│ │ │ ├── sub-C001_space-MNI152NLin2009cAsym_desc-synthstrip_dseg.nii.gz
│ │ │ ├── sub-C001_space-MNI152NLin2009cAsym_label-CSF_desc-synthstrip_probseg.nii.gz
│ │ │ ├── sub-C001_space-MNI152NLin2009cAsym_label-GM_desc-synthstrip_probseg.nii.gz
│ │ │ └── sub-C001_space-MNI152NLin2009cAsym_label-WM_desc-synthstrip_probseg.nii.gz
│ │ ├── figures
│ │ │ ├── sub-C001_desc-about_T1w.html
│ │ │ ├── sub-C001_desc-conform_T1w.html
│ │ │ ├── sub-C001_desc-reconall_T1w.svg
│ │ │ ├── sub-C001_desc-summary_T1w.html
│ │ │ ├── sub-C001_desc-synthstrip_dseg.svg
│ │ │ └── sub-C001_space-MNI152NLin2009cAsym_desc-synthstrip_T1w.svg
│ │ └── log
│ │ ├── 20221006-235807_a4ffd58c-5176-4f36-9898-65893067fff0
│ │ │ └── fmriprep.toml
│ │ └── 20221007-094420_1844f62d-44eb-474e-b188-8bfab0770b8c
│ │ └── fmriprep.toml
│ └── sub-C001.html
├── gradcorrect
│ ├── dataset_description.json
│ ├── participants.tsv
│ ├── sourcedata
│ │ ├── gradcorrect
│ │ │ └── sub-C001
│ │ │ ├── anat
│ │ │ ├── dwi
│ │ │ └── fmap
│ │ └── scratch
│ │ ├── sub-C001.1591035263.detjac.nii.gz
│ │ ├── sub-C001.1591035263.warp.nii.gz
│ │ ├── sub-C001.1614499974.detjac.nii.gz
│ │ ├── sub-C001.1614499974.warp.nii.gz
│ │ ├── sub-C001.243612401.detjac.nii.gz
│ │ ├── sub-C001.243612401.warp.nii.gz
│ │ ├── sub-C001.2655905243.detjac.nii.gz
│ │ ├── sub-C001.2655905243.warp.nii.gz
│ │ ├── sub-C001.2773381117.detjac.nii.gz
│ │ ├── sub-C001.2773381117.warp.nii.gz
│ │ ├── sub-C001.2955285821.detjac.nii.gz
│ │ ├── sub-C001.2955285821.graddev.nii.gz
│ │ ├── sub-C001.2955285821.warp.nii.gz
│ │ ├── sub-C001.3541686064.detjac.nii.gz
│ │ ├── sub-C001.3541686064.warp.nii.gz
│ │ ├── sub-C001.4173290510.detjac.nii.gz
│ │ ├── sub-C001.4173290510.warp.nii.gz
│ │ ├── sub-C001.702483272.detjac.nii.gz
│ │ ├── sub-C001.702483272.warp.nii.gz
│ │ ├── sub-C001.710399540.detjac.nii.gz
│ │ └── sub-C001.710399540.warp.nii.gz
│ └── sub-C001
│ ├── anat
│ │ ├── sub-C001_acq-MP2RAGE_run-01_T1map.json
│ │ ├── sub-C001_acq-MP2RAGE_run-01_T1map.nii.gz
│ │ ├── sub-C001_acq-MP2RAGE_run-01_T1w.json
│ │ ├── sub-C001_acq-MP2RAGE_run-01_T1w.nii.gz
│ │ ├── sub-C001_acq-SPACE_run-01_T2w.json
│ │ ├── sub-C001_acq-SPACE_run-01_T2w.nii.gz
│ │ ├── sub-C001_acq-TOF_angio.json
│ │ ├── sub-C001_acq-TOF_angio.nii.gz
│ │ ├── sub-C001_acq-TSEcor_run-01_T2w.json
│ │ ├── sub-C001_acq-TSEcor_run-01_T2w.nii.gz
│ │ ├── sub-C001_acq-TSEtra_run-01_T2w.json
│ │ ├── sub-C001_acq-TSEtra_run-01_T2w.nii.gz
│ │ ├── sub-C001_acq-TSEtra_run-02_T2w.json
│ │ ├── sub-C001_acq-TSEtra_run-02_T2w.nii.gz
│ │ ├── sub-C001_acq-UNI_run-01_MP2RAGE.json
│ │ ├── sub-C001_acq-UNI_run-01_MP2RAGE.nii.gz
│ │ ├── sub-C001_inv-1_run-01_MP2RAGE.json
│ │ ├── sub-C001_inv-1_run-01_MP2RAGE.nii.gz
│ │ ├── sub-C001_inv-2_run-01_MP2RAGE.json
│ │ ├── sub-C001_inv-2_run-01_MP2RAGE.nii.gz
│ │ ├── sub-C001_part-mag_echo-1_GRE.json
│ │ ├── sub-C001_part-mag_echo-1_GRE.nii.gz
│ │ ├── sub-C001_part-mag_echo-2_GRE.json
│ │ ├── sub-C001_part-mag_echo-2_GRE.nii.gz
│ │ ├── sub-C001_part-mag_echo-3_GRE.json
│ │ ├── sub-C001_part-mag_echo-3_GRE.nii.gz
│ │ ├── sub-C001_part-mag_echo-4_GRE.json
│ │ ├── sub-C001_part-mag_echo-4_GRE.nii.gz
│ │ ├── sub-C001_part-phase_echo-1_GRE.json
│ │ ├── sub-C001_part-phase_echo-1_GRE.nii.gz
│ │ ├── sub-C001_part-phase_echo-2_GRE.json
│ │ ├── sub-C001_part-phase_echo-2_GRE.nii.gz
│ │ ├── sub-C001_part-phase_echo-3_GRE.json
│ │ ├── sub-C001_part-phase_echo-3_GRE.nii.gz
│ │ ├── sub-C001_part-phase_echo-4_GRE.json
│ │ └── sub-C001_part-phase_echo-4_GRE.nii.gz
│ ├── dwi
│ │ ├── sub-C001_run-01_dwi.bval
│ │ ├── sub-C001_run-01_dwi.bvec
│ │ ├── sub-C001_run-01_dwi.json
│ │ ├── sub-C001_run-01_dwi.nii.gz
│ │ ├── sub-C001_run-02_dwi.bval
│ │ ├── sub-C001_run-02_dwi.bvec
│ │ ├── sub-C001_run-02_dwi.json
│ │ ├── sub-C001_run-02_dwi.nii.gz
│ │ ├── sub-C001_run-03_dwi.bval
│ │ ├── sub-C001_run-03_dwi.bvec
│ │ ├── sub-C001_run-03_dwi.json
│ │ └── sub-C001_run-03_dwi.nii.gz
│ ├── fmap
│ │ ├── sub-C001_acq-b1Div_SA2RAGE.json
│ │ ├── sub-C001_acq-b1Div_SA2RAGE.nii.gz
│ │ ├── sub-C001_acq-b1map_SA2RAGE.json
│ │ ├── sub-C001_acq-b1map_SA2RAGE.nii.gz
│ │ ├── sub-C001_inv-1_SA2RAGE.json
│ │ ├── sub-C001_inv-1_SA2RAGE.nii.gz
│ │ ├── sub-C001_inv-2_SA2RAGE.json
│ │ ├── sub-C001_inv-2_SA2RAGE.nii.gz
│ │ ├── sub-C001_magnitude1.json
│ │ ├── sub-C001_magnitude1.nii.gz
│ │ ├── sub-C001_magnitude2.json
│ │ ├── sub-C001_magnitude2.nii.gz
│ │ ├── sub-C001_phasediff.json
│ │ └── sub-C001_phasediff.nii.gz
│ └── sub-C001_scans.tsv
└── synthstrip
├── dataset_description.json
└── sub-C001
└── anat
├── sub-C001_desc-synthstrip_T1w.nii.gz
└── sub-C001_space-T1w_brainmask.nii.gz
https://github.com/khanlab/gradcorrect
Sriranga Kashyap. (2021). srikash/3dMPRAGEise: ondu (1.0). Zenodo. https://doi.org/10.5281/zenodo.4626825
Cox RW (1996). AFNI: software for analysis and visualization of functional magnetic resonance neuroimages. Comput Biomed Res 29(3):162-173. doi:10.1006/cbmr.1996.0014 https://pubmed.ncbi.nlm.nih.gov/8812068/
RW Cox, JS Hyde (1997). Software tools for analysis and visualization of FMRI Data. NMR in Biomedicine, 10: 171-178. https://pubmed.ncbi.nlm.nih.gov/9430344/
Hoopes A, Mora JS, Dalca AV, Fischl B, Hoffmann M. SynthStrip: skull-stripping for any brain image. Neuroimage. 2022 Oct 15;260:119474. doi: 10.1016/j.neuroimage.2022.119474. Epub 2022 Jul 13. PMID: 35842095; PMCID: PMC9465771.
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Dickie EW, Anticevic A, Smith DE, Coalson TS, Manogaran M, Calarco N, Viviano JD, Glasser MF, Van Essen DC, Voineskos AN. Ciftify: A framework for surface-based analysis of legacy MR acquisitions. Neuroimage. 2019 Aug 15;197:818-826. doi: 10.1016/j.neuroimage.2019.04.078. Epub 2019 May 12. PMID: 31091476; PMCID: PMC6675413.