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.
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.eduwrote:
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.comwrote:
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
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.eduwrote:
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.comwrote:
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
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.eduwrote:
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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 _______________________________________________ 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
In my previous mail I sent you the FSLview screenshot( the .nii one)
ALso, I am attaching the original picture which was in BV. It shows system coordinates (which is RAS coordinates in BV). The position of the ROIs seem to be reversed when viewing with fslview. which is the space which FSlview displays?
Could this be a clue in the coordinate space issue?
I need to open this .nii in Freesurfer
Thanks
Barnali
On Wed, Apr 22, 2009 at 1:34 PM, Nick Schmansky nicks@nmr.mgh.harvard.eduwrote:
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 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://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
On Wed, Apr 22, 2009 at 1:34 PM, Nick Schmansky nicks@nmr.mgh.harvard.eduwrote:
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 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
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