p.s. probably you should use the ?h.BA.thresh.annot, which is the annot containing the labels thresholded to have the correct area
cheers Bruce On Mon, 8 Sep 2014, Bruce Fischl wrote: > 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 > > > _______________________________________________ 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.
