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