You can regenerate a wmparc that does not have the unsegmented wm with something like
cd $SUBJECTS_DIR/subject mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown --volmask --ctxseg aparc+aseg.mgz --wmparc-dmax 100 --o mri/wmparc2.mgz
Then create your lobes from that
On 01/27/2016 05:47 PM, VA Research wrote:
Hello FS experts,
Does anyone have some form of step-by-step instructions on how to do this ?
Thanks so much
Joseph Brainiac . wrote:
/Hi All, />//>/I need to classify WM into different lobes (temporal, parietal, />/frontal, occipital). I tried to do the lobe mapping using />/parcellations from wmparc.mgz. />/http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation />//>/My problem is the "unsegmented white matter" in wmparc.mgz. My />/understanding is that these unsegmented areas are classified so />/because they are beyond 5mm from any pre-classified cortex area. />//>/My questions: />/(1) So in order to classify "unsegmented WM" into lobes, do I need to />/take each voxel in the unsegmented WM region and then assign it to the />/closest cortex area to classify it into respective parcellations. Then />/re-group into lobes. Is this correct? / //>/(2) Are there any tailor made function or any other easier way to do />/this? Is there any easier way to segment WM into lobes directly that I />/have missed? />//>/Thanks, />/Brain/
You can do this in a couple of steps. First, you'll need to create a lobe annotation. You can do this in 3 ways: 1. mri_annotation2label --lobesStrict 2. mri_annotation2label --lobes 3. Custom: break up annotation and recombine: a. mri_annotation to create separate label files b. mri_mergelabels to create single label files for each lobe label c. mris_label2annot to create the lobe annotation
Next, create the WM segmentation with mri_aparc2aseg, specifying your new lobe annot and adding --labelwm. You can control the distance with --wmparc-dmax
doug
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