On Thu, 2009-04-16 at 13:36 -0700, Barnali Basu wrote:
> Hi
>
> We are trying to another method to open a BV ROI in FS. My colleague
> has sent me ROI generated in BV in Nifti format, which when I try to
> open in FS gives the following error
>
> barnali-work:/usr/local/freesurfer/subjects> tkmedit bert ROIs.nii
> WARNING: hdr.dim[4] = 0 (nframes), setting to 1
> niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm
> MRIresample(): error inverting matrix; determinant is nan, matrix is:
> nan nan nan nan;
> nan nan nan nan;
> nan nan nan nan;
> 0.000 0.000 0.000 1.000;
>
>
> Error: Loading volume ROIs.nii
>
> Couldn't read the anatomical volume.
>
> Tkmedit couldn't read the volume you specified.
> This could be because the image format wasn't recognized,
> or it couldn't find the proper header,
> or the file(s) were unreadable,
> or it was the wrong size.
>
> ********
>
> I even tried to convert it into .mgz .it throws the following error:
>
> barnali-work:/usr/local/freesurfer/subjects> mri_convert ROIs.nii
> ROIsNifti.mgz
> mri_convert ROIs.nii ROIsNifti.mgz
> $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $
> reading from ROIs.nii...
> WARNING: hdr.dim[4] = 0 (nframes), setting to 1
> niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (nan, nan, nan)
> j_ras = (nan, nan, nan)
> k_ras = (nan, nan, nan)
> Reslicing using trilinear interpolation
> MRIresample(): error inverting matrix; determinant is nan, matrix is:
> nan nan nan nan;
> nan nan nan nan;
> nan nan nan nan;
> 0.000 0.000 0.000 1.000;
>
> Any help?
>
>
> On Sat, Apr 11, 2009 at 3:05 PM, Bruce Fischl
> <
fischl@nmr.mgh.harvard.edu> wrote:
> 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.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.
>
>
>
> --
> Barnali Basu
>
> Cell : 425 638 2936
> Home: 206 257 0174
>
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>
>
>
>
>
>
>
> --
> Barnali Basu
>
> Cell : 425 638 2936
> Home: 206 257 0174
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