1. https://gsanroma.github.io/posts/2019/01/vbm-data-preparation/
2. https://ftp.nmr.mgh.harvard.edu/pub/dist/freesurfer/tutorial_packages/centos6/fsl_507/doc/wiki/FSLVBM

1. Get GM & WM
2. Make initial template in MNI space
3. Register to initial template & make custom template
4. Register to custom template
5. Merge and AVG
6. randomise!

I will get GM and WM from FS LUT.

My first step should be get the aseg file from Freesurfer. Not to hard, I should know the FS subject ID, the ID in the actual project and the working directory,

get_aseg.sh

#!/bin/sh
 
fsid=$1
shift
 
id=$1
shift
 
dir=$1
shift
 
debug=0
 
#First get the freesurfer processed aseg.mgz
${FREESURFER_HOME}/bin/mri_label2vol --seg ${SUBJECTS_DIR}/${fsid}/mri/aseg.mgz --temp ${SUBJECTS_DIR}/${fsid}/mri/rawavg.mgz --o ${dir}/${id}_tmp_aseg.mgz --regheader ${SUBJECTS_DIR}/${fsid}/mri/aseg.mgz
${FREESURFER_HOME}/bin/mri_convert --in_type mgz --out_type nii ${dir}/${id}_tmp_aseg.mgz ${dir}/${id}_tmp_aseg.nii.gz
${FSLDIR}/bin/fslreorient2std ${dir}/${id}_tmp_aseg ${dir}/${id}_aseg
 
if [ $debug = 0 ] ; then
    rm ${dir}/${id}_tmp* 
fi

And from the aseg file I will select the proper segmentations. So I will make a loop over the segmentation tags and run a simple script,

get_lut.sh

#!/bin/sh
 
id=$1
shift
 
dir=$1
shift
 
lut=$1
shift
 
debug=0
 
${FSLDIR}/bin/fslmaths ${dir}/${id}_aseg.nii.gz -uthr ${lut} -thr ${lut} -div ${lut} ${dir}/${id}_${lut}.nii.gz