Hi Barnali,
we never resample into tal coords, which is why you need to generate the
ROIs in native RAS space.
cheers,
Bruce
On Sat, 11 Apr 2009, Barnali Basu wrote:
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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
