Hi David what is the annot you are using in mris_label2annot? is it the ?h.BA.annot?
cheers Bruce On Mon, 8 Sep 2014, David Provencher wrote: > Hi, > > I am new to freesurfer and I am trying to figure our how to extract 3d > masks in native space for the visual cortex (BA 17,18,19) of individual > subjects. I have looked at other threads similar to this, but there are > still a few things I can't figure out in generating the masks (the > conversion to native space should be fine). > > 1- I ran recon-all and I have V1, V2 and MT labels. My knowledge of > brain anatomy is very limited, but if I understand correctly, this > equates to BA 17, 18 and V5, so I don't have access to all of B19 (V3, > V4 and V5), right? > > 2- I managed to convert V1, V2 and MT labels to 3d masks using > mri_label2vol and it seems to work at first glance when I looked at the > generated file with freeView. However, I read in the mailing list that > mri_label2vol produces "patchy" volumes and that it is preferable to use > mri_aparc2aseg instead. That's what I can't figure out. From what I > understand, mri_aparc2aseg aims to map the surface labels of interest to > the segmented volumes? I tried doing the following (I altered some file > names/paths for readability): > > # convert labels to annotation (outputs lh.myAnnot.annot & > rh.myAnnot.annot)) > mris_label2annot --s <subject> --h lh --l lh.V1.label --l lh.V2.label > ---l lh.label --ctab BA.ctab --a annot > mris_label2annot --s <subject> --h rh --l rh.V1.label --l rhV2.label > ---l rh.label --ctab BA.ctab --a annot > > # convert to volume > mri_aparc2aseg --s <subject> --annot myAnnot.annot --o lh.asegTest.mgz > > When I look at the asegTest.mgz file in freeView, I only see segmented > cortical volumes and I can't see anything related to V1, V2 or MT, so I > assume that I don't use mri_aparc2aseg correctly, but I can't manage to > make it work. > > Any help would be appreciated! > David > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ 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.
