Package that provides tools for brain MRI Deep Learning pre-processing.
Note
This page is a reference documentation. It only explains the function signature, and not how to use it. Please refer to the gallery for the big picture.
- brainprep.workflow.cat12vbm.brainprep_cat12vbm(anatomical, outdir, longitudinal=False, model_long=1, session=None, cat12='/opt/spm/standalone/cat_standalone.sh', spm12='/opt/spm', matlab='/opt/mcr/v93', tpm='/opt/spm/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii', darteltpm='/opt/spm/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_volumes/Template_1_IXI555_MNI152.nii', verbose=0)[source]ΒΆ
Define CAT12 VBM pre-processing workflow.
- Parameters:
anatomical : list or str
path to the anatomical T1w Nifti file, or if longitudinal data path to anatomical T1w Nifti files of one subject.
outdir : str
the destination folder for cat12vbm outputs.
session : str
the session names, usefull for longitudinal preprocessings. Warning session and nii files must be in the same order.
longitudinal : bool
optionally perform longitudinal CAT12 VBM process.
model_long : int
longitudinal model choice, default 1. 1 short time (weeks), 2 long time (years) between images sessions.
cat12 : str
path to the CAT12 standalone executable.
spm12 : str
the SPM12 folder of standalone version.
matlab : str
Matlab Compiler Runtime (MCR) folder.
tpm : str
path to the SPM TPM file.
darteltpm : str
path to the CAT12 template file.
verbose : int
control the verbosity level: 0 silent, [1, 2] verbose.
Follow us