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.quinn@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.basu@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.



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Barnali Basu

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Home: 206 257 0174

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Barnali Basu

Cell   : 425 638 2936
Home: 206 257 0174