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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
