Dear Experts,

I want to create some cortical and subcortical masks to use as seed regions in fsl’s Probtrackx and have faced some questions that ask you help me with them.

To extract subcortical regions I have used the below commands (e.g. for thalamus_r):

 {

mri_label2vol \

    --seg  $SUBJECT_DIR/${subject}/mri/aparc+aseg.mgz \

    --fillthresh  0 > /dev/null \

    --identity \

    --temp  $SUBJECT_DIR/${subject}/mri/orig.mgz \

    --o  ${datadir}/aparc+aseg.nii.gz \

 mri_binarize --i ${datadir}/aparc+aseg.nii.gz --match 49 --o ${datadir}/thalamus_r.nii.gz

}

I noticed that the number of voxels of the created masks in this way are different from which is written in aseg.stats file. Could you please explain the reason and the way to make these numbers as close as possible.

For cortical regions I used both the above and below commands (e.g. for rh.superiortemporal):

{

mri_annotation2label --subject ${subject} \

    --hemi rh \

    --annotation $SUBJECTS_DIR/${subject}/label/rh.aparc.annot \

    --outdir $SUBJECTS_DIR/${subject}/label \

    --surface white

 

mri_label2vol \

    --label $SUBJECTS_DIR/${subject}/label /rh.superiortemporal.label \

    --temp  $SUBJECT_DIR/${subject}/mri/orig.mgz \

    --identity \

    --o ${datadir}/rh.superiortemporal.nii.gz \

    --fillthresh 0 > /dev/null

}

Again I have noticed differences in number of voxels of the results from two methods for cortical regions and also a difference from aparc.stats’s numbers. My final goal in to use the masks in probtrackx to find the connections between subcortical structures and cortical regions in temporal lobe and I wonder which method is more accurate to create cortical masks. Also I want to know using which atlas is better for my purpose, aparc+aseg or aparc.a2009s+aseg.

Your help is greatly appreciated.

Wishes,