I have visualized SLF2 with DSI-studio but I want to visualize SLF-2 with MRTrix3 by creating a connectome map by giving labels such as Inferior-Parietal-Lobule and etc. instead of HCPMMP which I am used to work with untill now.
For creating an hcpmmp1_parcels_nocoreg.mif file, I was following the BATMAN tutorial and it was working great.
Is there a way of creating something like cortex_parcels_nocoreg.mif file, which involves parcels of cortex lobules instead of hcpmmp parcels.
Because If i create a such .csv file from that cortex_parcels_nocoreg.mif file, then I can get only SLF2 by using connectome2tck and “-nodes inferior parietal lobule, prefrontal cortex” option.
Does someone know how to implement it? I was using the following codeline for hcpmmp1_parcels_nocoreg.mif file
mri_surf2surf --srcsubject fsaverage --trgsubject SUBJ --hemi lh --sval-annot $SUBJECTS_DIR/fsaverage/label/lh.HCP-MMP1.annot --tval $SUBJECTS_DIR/SUBJ/label/lh.HCP-MMP1.annot
mri_surf2surf --srcsubject fsaverage --trgsubject SUBJ --hemi rh --sval-annot $SUBJECTS_DIR/fsaverage/label/rh.HCP-MMP1.annot --tval $SUBJECTS_DIR/SUBJ/label/rh.HCP-MMP1.annot
mri_aparc2aseg --old-ribbon --s SUBJ --annot HCP-MMP1 --o hcpmmp1.mgz
mrconvert –datatype uint32 hcpmmp1.mgz hcpmmp1.mif
labelconvert hcpmmp1.mif hcpmmp1_original.txt hcpmmp1_ordered.txt hcpmmp1_parcels_nocoreg.mif