Can someone HELP ME, I was generating connectome from diffusion mri, and It’s really strange that the shape adjacency matrix is (163*164).
I’ve tagged my code below:
#!/bin/bash
baseDir='/media/cmet-standard/d087db17-fa04-4471-b171-8138fae36357/Liu/ADNI/dmri/test1'
cd $baseDir
patList=$(ls $baseDir)
for patID in $patList
do
echo "Patient ID: $patID"
timepointlist=$(ls -d $baseDir/$patID/*/)
for timepoint in $timepointlist
do
targetDir=$timepoint
echo "Target directory: $targetDir"
if [ -d "$targetDir" ]; then
cd $targetDir
else
echo "Directory does not exist: $targetDir"
fi
mrconvert -fslgrad *.bvec *.bval *.nii.gz dwi.mif -force
#denoise
dwidenoise dwi.mif denoise.mif -force
mrdegibbs denoise.mif degibbs.mif -force
#alignment
dwiextract degibbs.mif -bzero - | mrmath -axis 3 - mean b0.nii -force
flirt.fsl -dof 6 -cost normmi -ref $baseDir/T1.nii.gz -in b0.nii -omat T_fsl.txt
echo "fishish flirt"
transformconvert T_fsl.txt b0.nii $baseDir/T1.mgz flirt_import T_DWItoT1.txt -force
mrtransform -linear T_DWItoT1.txt degibbs.mif align.mif -force # apply alignment
echo "fishish alignment"
#segmentation
mrconvert /home/cmet-standard/application/freesurfer/subjects/fsaverage/mri/aparc.a2009s+aseg.mgz aparc2009aseg.nii.gz -force # readable for MRtrix
5ttgen freesurfer aparc2009aseg.nii.gz 5ttseg.mif -force
# 5tt2gmwmi 5ttseg.mif 5tt_gmwmi.mif
echo "fishish segmentation"
#tractography
## single shell(only one b value)
# estimate response function for wm only for single shell
dwi2response tournier align.mif wm_ss.txt -force
dwi2fod csd align.mif wm_ss.txt dwi_wmCsd.mif -force
### diffusion tensor imagine ###
# create a mask
dwi2mask align.mif - | maskfilter - dilate dwi_mask.mif -force
# creatediffusion tensor
dwi2tensor -mask dwi_mask.mif align.mif dt.mif -force
# calculate eigenvectors and scalar metrics from tensor
tensor2metric dt.mif -fa dt_fa.mif -adc dt_adc.mif -force
#create ROIs
mrthreshold -abs 0.2 dt_fa.mif - | mrcalc - dwi_mask.mif -mult dwi_wmMask.mif
#whole brain tractography
tckgen -algo iFOD2 -act 5ttseg.mif -backtrack -crop_at_gmwmi \
-cutoff 0.03 -angle 60 -minlength 15 -maxlength 230 \
-seed_image dwi_wmMask.mif -select 200k \
dwi_wmCsd.mif\
fibs_200k_angles45_maxlength200_act.tck -force
echo "fishish tractography"
# connectome
# relabel the parcellation order
labelconvert aparc2009aseg.nii.gz $FREESURFER_HOME/FreeSurferColorLUT.txt \
/home/cmet-standard/anaconda3/share/mrtrix3/labelconvert/fs_a2009s.txt \
aparc+aseg_relabl.nii.gz -force
# generate connectome
tck2connectome -symmetric -zero_diagonal -scale_invnodevol \
fibs_200k_angles45_maxlength200_act.tck \
aparc+aseg_relabl.nii.gz \
connectome.csv \
-out_assignment assignments.csv -force
done
done
