thank you for that, but i'm confused on how to do the rest as well .
I now have the wmparc2 with unsegmented areas, how can we create the lobar regions and use those to parcelate the WM into lobar regions? On Wed, Jan 27, 2016 at 2:57 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > 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. > >
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