Hi Bruce,
First of all, thanks for the reply! There was a typo in my initial question, so I rewrote it to make it clearer :
# 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 myAnnot mris_label2annot --s <subject> --h rh --l rh.V1.label --l rh.V2.label --l rh.label --ctab BA.ctab --a myAnnot
# convert ?h.myAnnot.annot files to volume mri_aparc2aseg --s <subject> --annot myAnnot.annot --o mySeg.mgz
I had not noticed the ?h.BA.annot and ?h.BA.thresh.annot files so I was trying to create an annotation with the labels I was interested in (V1, V2, MT). Maybe I misunderstood what an annotation is, but I thought it was just a collection of labels. I'm not sure what the difference is between .thresh and "not .thresh" labels. Anyway, whether I run the code above or just the following :
# convert ?h.BA.annot to volume mri_aparc2aseg --s <subject> --annot BA --o BAseg.mgz
when I open the .mgz file in freeview, something is obviously wrong (see https://www.dropbox.com/s/evthp4sx40azost/BAseg.png?dl=0 and https://www.dropbox.com/s/s5s7wcwywlaq68o/mySeg.png?dl=0). In comparison, when I convert either the ?h.myAnnot.annot or ?h.BA.annot files using mri_label2vol, it seems fine (see https://www.dropbox.com/s/avo1ot8bitbaeeo/BAlabels.png?dl=0).
regards, David
On 14-09-08 10:37 AM, Bruce Fischl wrote:
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
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