anat_preproc

Snakebids pipeline for anatomical preprocessing with gradcorrect, 3dMPRAGEise, synthstrip, fMRIPrep and ciftify.

Inputs

• Bids dataset with:

  • MP2RAGE data (uni and inv2)
  • T2w (will be added soon)

• dependencies:

  • python:
  • snakebids: https://github.com/akhanf/snakebids
  • singularity containers:
  • AFNI: https://hub.docker.com/r/afni/afnimakebuild
  • Ciftify: https://hub.docker.com/r/tigrlab/fmriprep_ciftify
  • fMRIPrep: https://hub.docker.com/r/nipreps/fmriprep/
  • gradcorrect: https://hub.docker.com/r/khanlab/gradcorrect
  • synthstrip: https://hub.docker.com/r/freesurfer/synthstrip

Usage

1. 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 yourvirtualenvnamehere source yourvirtualenvnamehere/bin/activate pip install snakebids==0.6.2

  ```

  1. Change directory to anat_preproc/anat_preproc (to be in same directory as run.py file).

• cd anat_preproc/anat_preproc

1. 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

run options:

``` (snakemake) [myousif9@gra-login2 anatpreproc]$ python run.py -h usage: run.py [-h] [--pybidsdb-dir PYBIDSDB_DIR] [--reset-db] [--force-output] [--help-snakemake] [--participant-label PARTICIPANTLABEL [PARTICIPANTLABEL ...]] [--excludeparticipantlabel EXCLUDEPARTICIPANTLABEL [EXCLUDEPARTICIPANTLABEL ...]] [--derivatives DERIVATIVES [DERIVATIVES ...]] [--fslicense FSLICENSE] [--gradcoef GRADCOEF] [--filter-uni FILTERUNI [FILTERUNI ...]] [--filter-inv2 FILTERINV2 [FILTERINV2 ...]] [--wildcards-uni WILDCARDSUNI [WILDCARDSUNI ...]] [--wildcards-inv2 WILDCARDSINV2 [WILDCARDSINV2 ...]] [--path-uni PATHUNI] [--path-inv2 PATHINV2] bidsdir 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 PYBIDSDBDIR, --pybidsdbdir PYBIDSDBDIR Optional path to directory of SQLite databasefile for PyBIDS. If directory is passed and folder exists, indexing is skipped. If resetdb is called, indexing will persist --reset-db, --resetdb Reindex existing PyBIDS SQLite database --force-output, --forceoutput 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

bidsdir The directory with the input dataset formatted according to the BIDS standard. outputdir 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 PARTICIPANTLABEL [PARTICIPANTLABEL ...], --participantlabel PARTICIPANTLABEL [PARTICIPANTLABEL ...] The label(s) of the participant(s) that should be analyzed. The label corresponds to sub-<participantlabel> 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. --excludeparticipantlabel EXCLUDEPARTICIPANTLABEL [EXCLUDEPARTICIPANTLABEL ...], --exclude-participant-label EXCLUDEPARTICIPANTLABEL [EXCLUDEPARTICIPANTLABEL ...] The label(s) of the participant(s) that should be excluded. The label corresponds to sub- 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) --fslicense FSLICENSE, --fs-license FSLICENSE Provide path to freesurfer license text file. --gradcoef GRADCOEF, --grad-coef GRADCOEF 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 FILTERUNI [FILTERUNI ...], --filteruni FILTERUNI FILTER_UNI ... --filter-inv2 FILTERINV2 [FILTERINV2 ...], --filterinv2 FILTERINV2 FILTER_INV2 ...

INPUT WILDCARDS: File path entities to use as wildcards in snakemake

--wildcards-uni WILDCARDSUNI [WILDCARDSUNI ...], --wildcardsuni WILDCARDSUNI WILDCARDS_UNI ... --wildcards-inv2 WILDCARDSINV2 [WILDCARDSINV2 ...], --wildcardsinv2 WILDCARDSINV2 WILDCARDS_INV2 ...

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 PATHUNI, --pathuni PATHUNI --path-inv2 PATHINV2, --pathinv2 PATHINV2 Outputs ======== ### Directory structure for single subject run: anatpreprocgradientcorrtest/ ├── config ├── derivatives │   ├── 3dmprageise │   ├── ciftify │   ├── fmriprep │   ├── gradcorrect │   └── synthstrip ├── logs │   ├── slurm │   └── sub-C001 └── work ├── fmriprep └── sub-C001

```

Directory structure of derivatives:

``` derivatives/ ├── 3dmprageise │   └── sub-C001 │   └── anat │   └── sub-C001desc-mprageiseT1w.nii.gz ├── ciftify │   ├── qcreconall │   │   ├── asegAx.html │   │   ├── asegCor.html │   │   ├── asegSag.html │   │   ├── index.html │   │   ├── MNILM.html │   │   ├── MNILRDV.html │   │   ├── MNIsurfAx.html │   │   ├── MNIsurfCor.html │   │   ├── MNIsurfSag.html │   │   └── sub-C001 │   │   ├── aparc.png │   │   ├── asegAx.png │   │   ├── asegCor.png │   │   ├── asegSag.png │   │   ├── curv.png │   │   ├── MNILM.png │   │   ├── MNILRDV.png │   │   ├── MNIsurfAx.png │   │   ├── MNIsurfCor.png │   │   ├── MNIsurfSag.png │   │   ├── nativeLRDV.png │   │   ├── nativesurfAx.png │   │   ├── nativesurfCor.png │   │   ├── nativesurfSag.png │   │   ├── qc.html │   │   └── thickness.png │   ├── sub-C001 │   │   ├── ciftireconall.log │   │   ├── MNINonLinear │   │   │   ├── aparc.a2009s+aseg.nii.gz │   │   │   ├── aparc+aseg.nii.gz │   │   │   ├── brainmaskfs.nii.gz │   │   │   ├── fsaverageLR32k │   │   │   │   ├── sub-C001.32kfsLR.wb.spec │   │   │   │   ├── sub-C001.aparc.32kfsLR.dlabel.nii │   │   │   │   ├── sub-C001.aparc.a2009s.32kfsLR.dlabel.nii │   │   │   │   ├── sub-C001.aparc.DKTatlas.32kfsLR.dlabel.nii │   │   │   │   ├── sub-C001.ArealDistortionFS.32kfsLR.dscalar.nii │   │   │   │   ├── sub-C001.ArealDistortionMSMSulc.32kfsLR.dscalar.nii │   │   │   │   ├── sub-C001.BAexvivo.32kfsLR.dlabel.nii │   │   │   │   ├── sub-C001.curvature.32kfsLR.dscalar.nii │   │   │   │   ├── sub-C001.EdgeDistortionMSMSulc.32kfsLR.dscalar.nii │   │   │   │   ├── sub-C001.L.atlasroi.32kfsLR.shape.gii │   │   │   │   ├── sub-C001.L.flat.32kfsLR.surf.gii │   │   │   │   ├── sub-C001.L.inflated.32kfsLR.surf.gii │   │   │   │   ├── sub-C001.L.midthickness.32kfsLR.surf.gii │   │   │   │   ├── sub-C001.L.pial.32kfsLR.surf.gii │   │   │   │   ├── sub-C001.L.sphere.32kfsLR.surf.gii │   │   │   │   ├── sub-C001.L.veryinflated.32kfsLR.surf.gii │   │   │   │   ├── sub-C001.L.white.32kfsLR.surf.gii │   │   │   │   ├── sub-C001.R.atlasroi.32kfsLR.shape.gii │   │   │   │   ├── sub-C001.R.flat.32kfsLR.surf.gii │   │   │   │   ├── sub-C001.R.inflated.32kfsLR.surf.gii │   │   │   │   ├── sub-C001.R.midthickness.32kfsLR.surf.gii │   │   │   │   ├── sub-C001.R.pial.32kfsLR.surf.gii │   │   │   │   ├── sub-C001.R.sphere.32kfsLR.surf.gii │   │   │   │   ├── sub-C001.R.veryinflated.32kfsLR.surf.gii │   │   │   │   ├── sub-C001.R.white.32kfsLR.surf.gii │   │   │   │   ├── sub-C001.sulc.32kfsLR.dscalar.nii │   │   │   │   └── sub-C001.thickness.32kfsLR.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.ArealDistortionFS.native.dscalar.nii │   │   │   │   ├── sub-C001.ArealDistortionMSMSulc.native.dscalar.nii │   │   │   │   ├── sub-C001.BAexvivo.native.dlabel.nii │   │   │   │   ├── sub-C001.curvature.native.dscalar.nii │   │   │   │   ├── sub-C001.EdgeDistortionMSMSulc.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.regLR.native.surf.gii │   │   │   │   ├── sub-C001.L.sphere.rot.native.surf.gii │   │   │   │   ├── sub-C001.L.veryinflated.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.regLR.native.surf.gii │   │   │   │   ├── sub-C001.R.sphere.rot.native.surf.gii │   │   │   │   ├── sub-C001.R.veryinflated.native.surf.gii │   │   │   │   ├── sub-C001.R.white.native.surf.gii │   │   │   │   ├── sub-C001.sulc.native.dscalar.nii │   │   │   │   └── sub-C001.thickness.native.dscalar.nii │   │   │   ├── Results │   │   │   ├── ROIs │   │   │   │   ├── AtlasROIs.2.nii.gz │   │   │   │   └── ROIs.2.nii.gz │   │   │   ├── sub-C001.164kfsLR.wb.spec │   │   │   ├── sub-C001.aparc.164kfsLR.dlabel.nii │   │   │   ├── sub-C001.aparc.a2009s.164kfsLR.dlabel.nii │   │   │   ├── sub-C001.aparc.DKTatlas.164kfsLR.dlabel.nii │   │   │   ├── sub-C001.ArealDistortionFS.164kfsLR.dscalar.nii │   │   │   ├── sub-C001.ArealDistortionMSMSulc.164kfsLR.dscalar.nii │   │   │   ├── sub-C001.BAexvivo.164kfsLR.dlabel.nii │   │   │   ├── sub-C001.curvature.164kfsLR.dscalar.nii │   │   │   ├── sub-C001.EdgeDistortionMSMSulc.164kfsLR.dscalar.nii │   │   │   ├── sub-C001.L.atlasroi.164kfsLR.shape.gii │   │   │   ├── sub-C001.L.flat.164kfsLR.surf.gii │   │   │   ├── sub-C001.L.inflated.164kfsLR.surf.gii │   │   │   ├── sub-C001.L.midthickness.164kfsLR.surf.gii │   │   │   ├── sub-C001.L.pial.164kfsLR.surf.gii │   │   │   ├── sub-C001.L.sphere.164kfsLR.surf.gii │   │   │   ├── sub-C001.L.veryinflated.164kfsLR.surf.gii │   │   │   ├── sub-C001.L.white.164kfsLR.surf.gii │   │   │   ├── sub-C001.R.atlasroi.164kfsLR.shape.gii │   │   │   ├── sub-C001.R.flat.164kfsLR.surf.gii │   │   │   ├── sub-C001.R.inflated.164kfsLR.surf.gii │   │   │   ├── sub-C001.R.midthickness.164kfsLR.surf.gii │   │   │   ├── sub-C001.R.pial.164kfsLR.surf.gii │   │   │   ├── sub-C001.R.sphere.164kfsLR.surf.gii │   │   │   ├── sub-C001.R.veryinflated.164kfsLR.surf.gii │   │   │   ├── sub-C001.R.white.164kfsLR.surf.gii │   │   │   ├── sub-C001.sulc.164kfsLR.dscalar.nii │   │   │   ├── sub-C001.thickness.164kfsLR.dscalar.nii │   │   │   ├── T1w.nii.gz │   │   │   ├── wmparc.nii.gz │   │   │   └── xfms │   │   │   ├── NonlinearRegfromlinear.log │   │   │   ├── Standard2T1wwarpnoaffine.nii.gz │   │   │   ├── T1w2StandardLinear.mat │   │   │   └── T1w2Standardwarpnoaffine.nii.gz │   │   └── T1w │   │   ├── aparc.a2009s+aseg.nii.gz │   │   ├── aparc+aseg.nii.gz │   │   ├── brainmaskfs.nii.gz │   │   ├── fsaverageLR32k │   │   │   ├── sub-C001.32kfsLR.wb.spec │   │   │   ├── sub-C001.L.inflated.32kfsLR.surf.gii │   │   │   ├── sub-C001.L.midthickness.32kfsLR.surf.gii │   │   │   ├── sub-C001.L.pial.32kfsLR.surf.gii │   │   │   ├── sub-C001.L.sphere.32kfsLR.surf.gii │   │   │   ├── sub-C001.L.veryinflated.32kfsLR.surf.gii │   │   │   ├── sub-C001.L.white.32kfsLR.surf.gii │   │   │   ├── sub-C001.R.inflated.32kfsLR.surf.gii │   │   │   ├── sub-C001.R.midthickness.32kfsLR.surf.gii │   │   │   ├── sub-C001.R.pial.32kfsLR.surf.gii │   │   │   ├── sub-C001.R.sphere.32kfsLR.surf.gii │   │   │   ├── sub-C001.R.veryinflated.32kfsLR.surf.gii │   │   │   └── sub-C001.R.white.32kfsLR.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.veryinflated.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.veryinflated.native.surf.gii │   │   │   └── sub-C001.R.white.native.surf.gii │   │   ├── T1wbrain.nii.gz │   │   ├── T1w.nii.gz │   │   └── wmparc.nii.gz │   └── zztemplates │   ├── AtlasROIs.2.nii.gz │   ├── colin.cerebral.L.flat.164kfsLR.surf.gii │   ├── colin.cerebral.L.flat.32kfsLR.surf.gii │   ├── colin.cerebral.R.flat.164kfsLR.surf.gii │   ├── colin.cerebral.R.flat.32kfsLR.surf.gii │   ├── fsaverage.LLR.sphericalstd.164kfsLR.surf.gii │   ├── fsaverage.RLR.sphericalstd.164kfsLR.surf.gii │   ├── L.atlasroi.164kfsLR.shape.gii │   ├── L.atlasroi.32kfsLR.shape.gii │   ├── L.sphere.32kfsLR.surf.gii │   ├── R.atlasroi.164kfsLR.shape.gii │   ├── R.atlasroi.32kfsLR.shape.gii │   └── R.sphere.32kfsLR.surf.gii ├── fmriprep │   ├── datasetdescription.json │   ├── desc-aparcasegdseg.tsv │   ├── desc-asegdseg.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-C001desc-aparcasegdseg.nii.gz │   │   │   ├── sub-C001desc-asegdseg.nii.gz │   │   │   ├── sub-C001desc-brainmask.json │   │   │   ├── sub-C001desc-brainmask.nii.gz │   │   │   ├── sub-C001desc-preprocT1w.json │   │   │   ├── sub-C001desc-preprocT1w.nii.gz │   │   │   ├── sub-C001desc-synthstripdseg.nii.gz │   │   │   ├── sub-C001from-fsnativeto-T1wmode-imagexfm.txt │   │   │   ├── sub-C001from-MNI152NLin2009cAsymto-T1wmode-imagexfm.h5 │   │   │   ├── sub-C001from-T1wto-fsnativemode-imagexfm.txt │   │   │   ├── sub-C001from-T1wto-MNI152NLin2009cAsymmode-imagexfm.h5 │   │   │   ├── sub-C001hemi-Linflated.surf.gii │   │   │   ├── sub-C001hemi-Lmidthickness.surf.gii │   │   │   ├── sub-C001hemi-Lpial.surf.gii │   │   │   ├── sub-C001hemi-Lsmoothwm.surf.gii │   │   │   ├── sub-C001hemi-Rinflated.surf.gii │   │   │   ├── sub-C001hemi-Rmidthickness.surf.gii │   │   │   ├── sub-C001hemi-Rpial.surf.gii │   │   │   ├── sub-C001hemi-Rsmoothwm.surf.gii │   │   │   ├── sub-C001label-CSFdesc-synthstripprobseg.nii.gz │   │   │   ├── sub-C001label-GMdesc-synthstripprobseg.nii.gz │   │   │   ├── sub-C001label-WMdesc-synthstripprobseg.nii.gz │   │   │   ├── sub-C001space-MNI152NLin2009cAsymdesc-brainmask.json │   │   │   ├── sub-C001space-MNI152NLin2009cAsymdesc-brainmask.nii.gz │   │   │   ├── sub-C001space-MNI152NLin2009cAsymdesc-preprocT1w.json │   │   │   ├── sub-C001space-MNI152NLin2009cAsymdesc-preprocT1w.nii.gz │   │   │   ├── sub-C001space-MNI152NLin2009cAsymdesc-synthstripdseg.nii.gz │   │   │   ├── sub-C001space-MNI152NLin2009cAsymlabel-CSFdesc-synthstripprobseg.nii.gz │   │   │   ├── sub-C001space-MNI152NLin2009cAsymlabel-GMdesc-synthstripprobseg.nii.gz │   │   │   └── sub-C001space-MNI152NLin2009cAsymlabel-WMdesc-synthstripprobseg.nii.gz │   │   ├── figures │   │   │   ├── sub-C001desc-aboutT1w.html │   │   │   ├── sub-C001desc-conformT1w.html │   │   │   ├── sub-C001desc-reconallT1w.svg │   │   │   ├── sub-C001desc-summaryT1w.html │   │   │   ├── sub-C001desc-synthstripdseg.svg │   │   │   └── sub-C001space-MNI152NLin2009cAsymdesc-synthstripT1w.svg │   │   └── log │   │   ├── 20221006-235807a4ffd58c-5176-4f36-9898-65893067fff0 │   │   │   └── fmriprep.toml │   │   └── 20221007-0944201844f62d-44eb-474e-b188-8bfab0770b8c │   │   └── fmriprep.toml │   └── sub-C001.html ├── gradcorrect │   ├── datasetdescription.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-C001acq-MP2RAGErun-01T1map.json │   │   ├── sub-C001acq-MP2RAGErun-01T1map.nii.gz │   │   ├── sub-C001acq-MP2RAGErun-01T1w.json │   │   ├── sub-C001acq-MP2RAGErun-01T1w.nii.gz │   │   ├── sub-C001acq-SPACErun-01T2w.json │   │   ├── sub-C001acq-SPACErun-01T2w.nii.gz │   │   ├── sub-C001acq-TOFangio.json │   │   ├── sub-C001acq-TOFangio.nii.gz │   │   ├── sub-C001acq-TSEcorrun-01T2w.json │   │   ├── sub-C001acq-TSEcorrun-01T2w.nii.gz │   │   ├── sub-C001acq-TSEtrarun-01T2w.json │   │   ├── sub-C001acq-TSEtrarun-01T2w.nii.gz │   │   ├── sub-C001acq-TSEtrarun-02T2w.json │   │   ├── sub-C001acq-TSEtrarun-02T2w.nii.gz │   │   ├── sub-C001acq-UNIrun-01MP2RAGE.json │   │   ├── sub-C001acq-UNIrun-01MP2RAGE.nii.gz │   │   ├── sub-C001inv-1run-01MP2RAGE.json │   │   ├── sub-C001inv-1run-01MP2RAGE.nii.gz │   │   ├── sub-C001inv-2run-01MP2RAGE.json │   │   ├── sub-C001inv-2run-01MP2RAGE.nii.gz │   │   ├── sub-C001part-magecho-1GRE.json │   │   ├── sub-C001part-magecho-1GRE.nii.gz │   │   ├── sub-C001part-magecho-2GRE.json │   │   ├── sub-C001part-magecho-2GRE.nii.gz │   │   ├── sub-C001part-magecho-3GRE.json │   │   ├── sub-C001part-magecho-3GRE.nii.gz │   │   ├── sub-C001part-magecho-4GRE.json │   │   ├── sub-C001part-magecho-4GRE.nii.gz │   │   ├── sub-C001part-phaseecho-1GRE.json │   │   ├── sub-C001part-phaseecho-1GRE.nii.gz │   │   ├── sub-C001part-phaseecho-2GRE.json │   │   ├── sub-C001part-phaseecho-2GRE.nii.gz │   │   ├── sub-C001part-phaseecho-3GRE.json │   │   ├── sub-C001part-phaseecho-3GRE.nii.gz │   │   ├── sub-C001part-phaseecho-4GRE.json │   │   └── sub-C001part-phaseecho-4GRE.nii.gz │   ├── dwi │   │   ├── sub-C001run-01dwi.bval │   │   ├── sub-C001run-01dwi.bvec │   │   ├── sub-C001run-01dwi.json │   │   ├── sub-C001run-01dwi.nii.gz │   │   ├── sub-C001run-02dwi.bval │   │   ├── sub-C001run-02dwi.bvec │   │   ├── sub-C001run-02dwi.json │   │   ├── sub-C001run-02dwi.nii.gz │   │   ├── sub-C001run-03dwi.bval │   │   ├── sub-C001run-03dwi.bvec │   │   ├── sub-C001run-03dwi.json │   │   └── sub-C001run-03dwi.nii.gz │   ├── fmap │   │   ├── sub-C001acq-b1DivSA2RAGE.json │   │   ├── sub-C001acq-b1DivSA2RAGE.nii.gz │   │   ├── sub-C001acq-b1mapSA2RAGE.json │   │   ├── sub-C001acq-b1mapSA2RAGE.nii.gz │   │   ├── sub-C001inv-1SA2RAGE.json │   │   ├── sub-C001inv-1SA2RAGE.nii.gz │   │   ├── sub-C001inv-2SA2RAGE.json │   │   ├── sub-C001inv-2SA2RAGE.nii.gz │   │   ├── sub-C001magnitude1.json │   │   ├── sub-C001magnitude1.nii.gz │   │   ├── sub-C001magnitude2.json │   │   ├── sub-C001magnitude2.nii.gz │   │   ├── sub-C001phasediff.json │   │   └── sub-C001phasediff.nii.gz │   └── sub-C001scans.tsv └── synthstrip ├── datasetdescription.json └── sub-C001 └── anat ├── sub-C001desc-synthstripT1w.nii.gz └── sub-C001space-T1w_brainmask.nii.gz

``` Citations ========= ### gradcorrect https://github.com/khanlab/gradcorrect ### 3dMPRAGEise: Sriranga Kashyap. (2021). srikash/3dMPRAGEise: ondu (1.0). Zenodo. https://doi.org/10.5281/zenodo.4626825

### AFNI:

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/

### SynthStrip: 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. ### Freesurfer: Fischl B. FreeSurfer. Neuroimage. 2012 Aug 15;62(2):774-81. doi: 10.1016/j.neuroimage.2012.01.021. Epub 2012 Jan 10. PMID: 22248573; PMCID: PMC3685476.

### fMRIPrep: Esteban O, Markiewicz CJ, Blair RW, Moodie CA, Isik AI, Erramuzpe A, Kent JD, Goncalves M, DuPre E, Snyder M, Oya H, Ghosh SS, Wright J, Durnez J, Poldrack RA, Gorgolewski KJ. fMRIPrep: a robust preprocessing pipeline for functional MRI. Nat Methods. 2019 Jan;16(1):111-116. doi: 10.1038/s41592-018-0235-4. Epub 2018 Dec 10. PMID: 30532080; PMCID: PMC6319393.

### Ciftify: 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.