Thanks Brian for the quick response. I have not generated labels in FS, I am trying to bring BV generated ROIs onto Freesurfer and make them coincide( for that, I understand both FS and BV have to be in same space). The BV Roi was generated in TAL. As far as I understand, trying to open TAL ROIs in non-TAL space should not work. You say,(your point no.2) that coordinates in label file need to be in RAS, not TAL. So will it work if I get the BV generated ROI files in RAS?
Also, one of my advisors suggested that I convert BV roi masks to Nifti, and then open them is FS. Is it possible? If so, how? (Will it still require getting BV Coordinates in RAS? ) All the space confusion arise because tools differ. I was under the impression that the inflated brain (after aurorecon- 2) is in TAL space (since in autorecon1 i had to do manual talairaching using tkregister), so I got my colleague generate all her BV ROis in TAL. Why is it that coordinates in label file need to be in RAS? Sorry If I am confusing you too. Thanks Barnali On Thu, Apr 9, 2009 at 5:00 PM, Brian T. Quinn <brian.t.qu...@nyu.edu>wrote: > hi Barnali- > > a good place to start is here: > http://surfer.nmr.mgh.harvard.edu/fswiki/LabelsClutsAnnotationFiles > > at least 2 things need to be corrected: > 1.the first value in each row of the label file must be a vertex number > from the FS surface (yours look like line numbers). I don't know if the > vertex numbers from your BV surf. and FS surf. match (my guess is they > don't). for labels generated in volume space in FS, this value can be -1 for > all vertex numbers. try using that and visualizing the label on the surface > (you may need to dilate/erode to close holes). but first: > > 2.i believe the coordinates in the label file need to be in RAS, not > talairach. > http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems > > good luck, > brian > > On Thu, Apr 9, 2009 at 5:46 PM, Barnali Basu <barnali.b...@gmail.com>wrote: > >> Hello >> >> Thanks for your previous responses. Those have been helpful. >> >> I have been trying to use some ROIs generated in BrainVoyager(BV). I have >> converted the ROI text file of BV to Freesurfer label text file format, >> using a small perl script (attached as testperl.txt). >> I am also attaching the original BV ROI file and the changed FS label file >> for your reference. >> >> My method seemed to work( no error), however all the ROIs , regardless of >> where they should be ( like frontal, MT etc) are landing up on the occipital >> area, including the occipital ROI itself. >> >> The BV ROI data sent to me was generated in Tal space, also, I have done >> manual Talairaching to the same data in FS using tkregister2. So I assume >> both versions of the subject (BV and FS) are in same space. Am I right? >> >> It would be great if you could suggest me where I must be going wrong. >> FYI, the BV processing has been done on a windows machine and sent to me. I >> work only on FS on Ubuntu. >> >> I am also attaching pictures of frontal and an occipital ROI on the >> inflated brain. >> >> Looking forward to some help. >> >> >> >> -- >> Barnali Basu >> >> Cell : 425 638 2936 >> Home: 206 257 0174 >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > -- Barnali Basu Cell : 425 638 2936 Home: 206 257 0174
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