Barnali, Does the ROIs.nii volume open and display correctly in fslview?
Nick 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 > <fis...@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.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 > _______________________________________________ > 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
