Commit f2f95182 authored by Jiewon's avatar Jiewon
Browse files

protocol

parent 8a07fd7a
# One slice #
mkdir -p oneslice
fslroi $data oneslice/data 0 -1 144 1 0 -1 0 -1
fslroi Concat_all_sessions/nodif_brain_mask oneslice/nodif_brain_mask 0 -1 144 1 0 -1
cp $bval oneslice/bvals
cp $bvec oneslice/bvecs
# Get brain mask - work on lowres then upsample in the end #
mkdir -p lowres
d=Concat_all_sessions
# Lower the resolution of powder
flirt -in $d/powder -out lowres/powder -applyisoxfm 2 -ref $d/powder
# Extract lowres powder brain mask
fslroi lowres powder lowres nodif 0 1
# Additional BET on brain mask
bet lowres/nodif lowres/nodif_brain -m -c 56 58 29 -f .2
flirt -in lowres/nodif_brain_mask -ref $d/powder -out $d/nodif_brain_mask -applyxfm -init $FSLDIR/etc/flirtsch/ident.mat -interp nearestneighbour # Upsample mask
# Bias field correction - on single slice #
fslroi oneslice/powder.nii.gz oneslice/nodif 0 1 # Single slice of powder
fast -n 1 -t 2 -b -B -o oneslice/fast oneslice/nodif # Fast get bias field
fslmaths oneslice/data -div oneslice/fast_bias oneslice/data_restore # Restore data by correcting for bias field
# FOD fitting #
/home/fs0/saad/fit_odf.py --data oneslice/data_restore \
--mask oneslice/nodif_brain_mask \
--bvals oneslice/bvals --bvecs oneslice/bvecs \
--out oneslice/FOD_b2.5_restore --verbose --shell=2500
# Method A. run LAYNII on GM segmentation on T1, DWI (Powder/b0)
# Method B. Segment diffusion data directly
# Method A.1 WM/GM Segmentation to feed to LAYNII #
# calculate normalised dwis
fslmaths oneslice/powder -div oneslice/nodif oneslice/dwis
# extract b2500
fslroi oneslice/dwis oneslice/b2.5k 2 1 # extract b2500 from dwi single slice
fslmaths oneslice/b2.5k -mas oneslice/nodif_brain_mask oneslice/b2.5k_brain
# run fast
fast -n 4 -t 1 -b -p -v oneslice/b2.5k_brain # generate segmentations
# Method A.2 Try with the T1 #
fslmaths lowres/powder.nii.gz -div lowres/nodif -mas lowres/nodif_brain_mask lowres/dwis_brain
fslroi lowres/dwis_brain.nii.gz lowres/b2.5k_brain 2 1
t1=T1/MPRAGE0p7mm_ave_brain # High res T1
diff=lowres/b2.5k_brain
flirt -in $t1 -ref $diff -out lowres/t1_to_diff -dof 12 -omat lowres/t1_to_diff.mat
# Segment T1 with FAST #
fast -n 3 -t 1 -b -p -v lowres/t1_to_diff
# Apply xfm to segmentation to get it to diffusion space #
flirt -in lowres/t1_to_diff_seg -ref $diff -out lowres/seg_diffspace -init t1_to_diff.mat -applyxfm
# Install LAYNII tools
git clone --depth 1 https://github.com/layerfMRI/LAYNII
# Run LAYNII on that
./LN2_LAYERS -rim lowres/seg_diffspace -nr_layers 3 -equivol -iter_smooth 100
./LN2_RIMIFY -input lowres/seg_diffspace -innergm 2 -outergm 1 -gm 3
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