All parameters are saved to ini file for user to repeat the analysis easily after a while.
The details are explained in the following ini file, where # started sentence are comments. Except VBM-8, which can cover almost all pre-processing steps.
You can also check the most updated sample ini config file which corresponds to Dev version.
[HPC] | |
ncpu-per-node=1 | |
[anat] | |
run = 1 #1 means Yes, 0 means No | |
working-dir = anat # working directory | |
postfix = “” #postfix for working-dir | |
overwrite = 0 #0 means trying to continue from last time’s trying if files in progress exist, 1 means ignore all intermediate files and start all over again | |
clean-intermediates = 1 #clean intermediate files after calculation | |
#if template-brain is set, it has highest priority | |
#if not, try to use template-head | |
#if using template-head, if brain-mask specified, use it; if not, bet it. | |
#if non is set, use MNI152_T1_2MM_BRAIN | |
template-brain = $FSL_DIR/data/standard/MNI152_T1_2mm_brain.nii.gz #specify anat template to be the normalized template | |
template-head = $FSL_DIR/data/standard/MNI152_T1_2mm.nii.gz #specify anat template to be the normalized template | |
template-brain-mask = $FSL_DIR/data/standard/MNI152_T1_2mm_brain_mask.nii.gz #specify anat template to be the normalized template | |
refine = 0 # use 3-stages refinement for dof 6, 9, 12 | |
robust-affine = 1 # use robust dof 12 refinement | |
fnirt = 0 # run FNIRT | |
first = 0 # run FIRST sub-cortical segmentations | |
vbm = 0 #VBM/DARTEL instead of Xiaowei’s robust way | |
vbm-config-m = “” #blank means using default VBM config, user can upload the one tested in user’s computer | |
#Skull stripping part | |
brainmask = “” #user-specified brain mask, then will use this mask instead of doing skull stripping. If set ,this option will suppress the following strip option, blank means disabled | |
strip-cmd = “” #blank means using ROBEX as default | |
#strip=’bet %s brain.nii -r 90 -m; ln -s brain_mask.nii brain.msk.nii;’ #if not specified, use ROBEX as default, otherwise using the command line included, such as FSL bet, ‘3dSkullStrip’ to use AFNI’s 3dSkullStrip … | |
#example: (has to make sure there is a brain mask named as brain.msk.nii) | |
#strip=’bet %s brain.nii -r 90 -m; ln -s brain_mask.nii brain.msk.nii;’ | |
lesionmask = “” # user-perfect mask/ground truth mask for lesion in T1 space | |
lesion-smoothing-times-min-voxelsize = “” # by default 4, which means 4 times min voxel size as FWHM smoothing for lesion mask after normalization, it can kill the ring effect for non-smooth surface of lesion | |
hybrid-clinical-tool = 0 #1 if choosing hybrid clinical toolbox by Chris Rorden | |
enantiomorphic = 0 #1 if choosing enantiomorphic way instead of CostFunctionMasking which is default way if lesion mask is specified | |
no-tar-filelist= #a file list containing all filters, should append my default filters before setting the list param here | |
do-tar = 1 #keep in mind about re-runing the script and processing func need the option to be explicitly set if it is tar balled | |