protocol

DO.txt

+# 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
+