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