First you'll have to decide on which wm parcellations will go into which lobe. When you have that, then you can use mri_binarize with the --replace option to change the index of a given segmentation to that of the lobe
On 01/27/2016 07:00 PM, VA Research wrote:
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 <greve@nmr.mgh.harvard.edu mailto:greve@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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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 <mailto: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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