Hi
I used FreeSurfer to automatically segment subcortical structures, and I would now like to transfer the data to Matlab. I am looking for a way to load the coordinates of all structures (or, if it isn't possible, for each structure, by its number) to Matlab, in Talairach coordinates. Is this possible? If so - how can it be done?
I use BrainVoyager, not FSL, for analysis, and I would like to somehow use the segmentation from FreeSurfer for analysis in Matlab, in combination with data I have from BrainVoyager (the functional data). I don't necessarily need talairach coordinates, but otherwise I'm not sure how it would be possible to convert between FreeSurfer and BrainVoyager.
Any suggestions? Thanks! Aya
Hi Aya,
you should be able to convert our segmentations to Nifti, which I assume Brainvoyager can read. You can load any of our volumes into matlab with either MRIread.m or load_mgh.m and go from there.
cheers Bruce
On Wed, 27 Oct 2010, Aya Ben Yakov wrote:
Hi
I used FreeSurfer to automatically segment subcortical structures, and I would now like to transfer the data to Matlab. I am looking for a way to load the coordinates of all structures (or, if it isn't possible, for each structure, by its number) to Matlab, in Talairach coordinates. Is this possible? If so - how can it be done?
I use BrainVoyager, not FSL, for analysis, and I would like to somehow use the segmentation from FreeSurfer for analysis in Matlab, in combination with data I have from BrainVoyager (the functional data). I don't necessarily need talairach coordinates, but otherwise I'm not sure how it would be possible to convert between FreeSurfer and BrainVoyager.
Any suggestions? Thanks! Aya
I'm also interested in these segmentations for analysis in Matlab.
In particular, which volumes should be loaded to get the coordinates of the segmentations?
I assume the segmentation volumes are just indices (all voxel belonging to the same segment are assigned the same unique index), correct ?
--- Sincerly, Dr. Ørjan Bergmann
On Wed, Oct 27, 2010 at 14:25, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Aya,
you should be able to convert our segmentations to Nifti, which I assume Brainvoyager can read. You can load any of our volumes into matlab with either MRIread.m or load_mgh.m and go from there.
cheers Bruce
On Wed, 27 Oct 2010, Aya Ben Yakov wrote:
Hi
I used FreeSurfer to automatically segment subcortical structures, and I
would now like to transfer the data to Matlab. I am looking for a way to load the coordinates of all structures (or, if it isn't possible, for each structure, by its number) to Matlab, in Talairach coordinates. Is this possible? If so - how can it be done?
I use BrainVoyager, not FSL, for analysis, and I would like to somehow
use the segmentation from FreeSurfer for analysis in Matlab, in combination with data I have from BrainVoyager (the functional data). I don't necessarily need talairach coordinates, but otherwise I'm not sure how it would be possible to convert between FreeSurfer and BrainVoyager.
Any suggestions? Thanks! Aya
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
yes, and all the volumes have the same index structure, so you can load any of them. The aseg.mgz contains the labeled volume, with the label to structure name conversion in the FreeSurferColorLUT.txt
cheers Bruce
On Wed, 27 Oct 2010, [UTF-8] Ørjan Bergmann wrote:
I'm also interested in these segmentations for analysis in Matlab.
In particular, which volumes should be loaded to get the coordinates of the segmentations?
I assume the segmentation volumes are just indices (all voxel belonging to the same segment are assigned the same unique index), correct ?
Sincerly, Dr. Ørjan Bergmann
On Wed, Oct 27, 2010 at 14:25, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Aya,
you should be able to convert our segmentations to Nifti, which I assume Brainvoyager can read. You can load any of our volumes into matlab with either MRIread.m or load_mgh.m and go from there.
cheers Bruce
On Wed, 27 Oct 2010, Aya Ben Yakov wrote:
Hi
I used FreeSurfer to automatically segment subcortical structures, and I
would now like to transfer the data to Matlab. I am looking for a way to load the coordinates of all structures (or, if it isn't possible, for each structure, by its number) to Matlab, in Talairach coordinates. Is this possible? If so - how can it be done?
I use BrainVoyager, not FSL, for analysis, and I would like to somehow
use the segmentation from FreeSurfer for analysis in Matlab, in combination with data I have from BrainVoyager (the functional data). I don't necessarily need talairach coordinates, but otherwise I'm not sure how it would be possible to convert between FreeSurfer and BrainVoyager.
Any suggestions? Thanks! Aya
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi I'm sorry for all these questions, but I'm very new to freesurfer, and I still don't really understand how things work. Is it necessary to convert to nifti? if I understand correctly, mri.vol should hold the needed information. In what space is this information (assuming some processing was done on the original data)? Can I convert it back to the original data space? or to talairach? The original data includes only 256X256X176, since there were only 176 slices, yet in mri.vol there are 256 slices. In short - how can I convert correctly to the original space and to talairach?
Thanks for your help! Aya
__________________________________________________
From Bruce Fischl fischl@nmr.mgh.harvard.edu
Sent Wed 10/27/2010 2:41 PM To Ørjan Bergmann orjan.bergmann@medisin.uio.no Cc freesurfer@nmr.mgh.harvard.edu Subject Re: [Freesurfer] subcortical structure coordinates
yes, and all the volumes have the same index structure, so you can load any of them. The aseg.mgz contains the labeled volume, with the label to structure name conversion in the FreeSurferColorLUT.txt
cheers Bruce
On Wed, 27 Oct 2010, [UTF-8] Ørjan Bergmann wrote:
I'm also interested in these segmentations for analysis in Matlab.
In particular, which volumes should be loaded to get the coordinates of the segmentations?
I assume the segmentation volumes are just indices (all voxel belonging to the same segment are assigned the same unique index), correct ?
Sincerly, Dr. Ørjan Bergmann
On Wed, Oct 27, 2010 at 14:25, Bruce Fischl <fischl@nmr.mgh.harvard.edu (mailto:fischl@nmr.mgh.harvard.edu)>wrote:
Hi Aya,
you should be able to convert our segmentations to Nifti, which I assume Brainvoyager can read. You can load any of our volumes into matlab with either MRIread.m or load_mgh.m and go from there.
cheers Bruce
On Wed, 27 Oct 2010, Aya Ben Yakov wrote:
Hi
I used FreeSurfer to automatically segment subcortical structures, and I
would now like to transfer the data to Matlab. I am looking for a way to load the coordinates of all structures (or, if it isn't possible, for each structure, by its number) to Matlab, in Talairach coordinates. Is this possible? If so - how can it be done?
I use BrainVoyager, not FSL, for analysis, and I would like to somehow
use the segmentation from FreeSurfer for analysis in Matlab, in combination with data I have from BrainVoyager (the functional data). I don't necessarily need talairach coordinates, but otherwise I'm not sure how it would be possible to convert between FreeSurfer and BrainVoyager.
Any suggestions? Thanks! Aya
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer)
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline (http://www.partners.org/complianceline) . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
__________________________________________________
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer)
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline (http://www.partners.org/complianceline) . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Aya,
you can convert the aseg back to the original voxel space with mri_convert. I think the cmdline would be:
mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg.rawavg.mgz
-rl = reslice like -rt = resample type
cheers Bruce
On Wed, 27 Oct 2010, Aya Ben Yakov wrote:
Hi I'm sorry for all these questions, but I'm very new to freesurfer, and I still don't really understand how things work. Is it necessary to convert to nifti? if I understand correctly, mri.vol should hold the needed information. In what space is this information (assuming some processing was done on the original data)? Can I convert it back to the original data space? or to talairach? The original data includes only 256X256X176, since there were only 176 slices, yet in mri.vol there are 256 slices. In short - how can I convert correctly to the original space and to talairach?
Thanks for your help! Aya
From Bruce Fischl fischl@nmr.mgh.harvard.edu Sent Wed 10/27/2010 2:41 PM To Ørjan Bergmann orjan.bergmann@medisin.uio.no Cc freesurfer@nmr.mgh.harvard.edu Subject Re: [Freesurfer] subcortical structure coordinates
yes, and all the volumes have the same index structure, so you can load any of them. The aseg.mgz contains the labeled volume, with the label to structure name conversion in the FreeSurferColorLUT.txt
cheers Bruce
On Wed, 27 Oct 2010, [UTF-8] Ørjan Bergmann wrote:
I'm also interested in these segmentations for analysis in Matlab.
In particular, which volumes should be loaded to get the coordinates of the segmentations?
I assume the segmentation volumes are just indices (all voxel belonging to the same segment are assigned the same unique index), correct ?
Sincerly, Dr. Ørjan Bergmann
On Wed, Oct 27, 2010 at 14:25, Bruce Fischl <fischl@nmr.mgh.harvard.edu (mailto:fischl@nmr.mgh.harvard.edu)>wrote:
Hi Aya,
you should be able to convert our segmentations to Nifti, which I assume Brainvoyager can read. You can load any of our volumes into matlab with either MRIread.m or load_mgh.m and go from there.
cheers Bruce
On Wed, 27 Oct 2010, Aya Ben Yakov wrote:
Hi
I used FreeSurfer to automatically segment subcortical structures, and I
would now like to transfer the data to Matlab. I am looking for a way to load the coordinates of all structures (or, if it isn't possible, for each structure, by its number) to Matlab, in Talairach coordinates. Is this possible? If so - how can it be done?
I use BrainVoyager, not FSL, for analysis, and I would like to somehow
use the segmentation from FreeSurfer for analysis in Matlab, in combination with data I have from BrainVoyager (the functional data). I don't necessarily need talairach coordinates, but otherwise I'm not sure how it would be possible to convert between FreeSurfer and BrainVoyager.
Any suggestions? Thanks! Aya
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer)
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline (http://www.partners.org/complianceline) . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer)
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline (http://www.partners.org/complianceline) . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Thanks! It seems to rotate the data, though. It does convert the data back to the original dimensions (256X256X176), ut the dimensions are switched. When I save the vol as nii and open in brainvoyager, the sagittal appears in coronal, etc. I tried switching the 256 dimensions, but it remains rotated (in a different rotation), so somehow the conversion to native space rotates the data. Any suggestions? Aya
__________________________________________________
From Bruce Fischl fischl@nmr.mgh.harvard.edu
Sent Wed 10/27/2010 3:48 PM To Aya Ben Yakov aya.benyakov@weizmann.ac.il Cc freesurfer@nmr.mgh.harvard.edu Subject Re: [Freesurfer] subcortical structure coordinates
Hi Aya,
you can convert the aseg back to the original voxel space with mri_convert. I think the cmdline would be:
mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg.rawavg.mgz
-rl = reslice like -rt = resample type
cheers Bruce
On Wed, 27 Oct 2010, Aya Ben Yakov wrote:
Hi I'm sorry for all these questions, but I'm very new to freesurfer, and I still don't really understand how things work. Is it necessary to convert to nifti? if I understand correctly, mri.vol should hold the needed information. In what space is this information (assuming some processing was done on the original data)? Can I convert it back to the original data space? or to talairach? The original data includes only 256X256X176, since there were only 176 slices, yet in mri.vol there are 256 slices. In short - how can I convert correctly to the original space and to talairach?
Thanks for your help! Aya
From Bruce Fischl <fischl@nmr.mgh.harvard.edu (mailto:fischl@nmr.mgh.harvard.edu)> Sent Wed 10/27/2010 2:41 PM To Ørjan Bergmann <orjan.bergmann@medisin.uio.no (mailto:orjan.bergmann@medisin.uio.no)> Cc freesurfer@nmr.mgh.harvard.edu (mailto:freesurfer@nmr.mgh.harvard.edu) Subject Re: [Freesurfer] subcortical structure coordinates
yes, and all the volumes have the same index structure, so you can load any of them. The aseg.mgz contains the labeled volume, with the label to structure name conversion in the FreeSurferColorLUT.txt
cheers Bruce
On Wed, 27 Oct 2010, [UTF-8] Ørjan Bergmann wrote:
I'm also interested in these segmentations for analysis in Matlab.
In particular, which volumes should be loaded to get the coordinates of the segmentations?
I assume the segmentation volumes are just indices (all voxel belonging to the same segment are assigned the same unique index), correct ?
Sincerly, Dr. Ørjan Bergmann
On Wed, Oct 27, 2010 at 14:25, Bruce Fischl <fischl@nmr.mgh.harvard.edu (mailto:fischl@nmr.mgh.harvard.edu) (mailto:fischl@nmr.mgh.harvard.edu)>wrote: (mailto:fischl@nmr.mgh.harvard.edu%29%3Ewrote:)
Hi Aya,
you should be able to convert our segmentations to Nifti, which I assume Brainvoyager can read. You can load any of our volumes into matlab with either MRIread.m or load_mgh.m and go from there.
cheers Bruce
On Wed, 27 Oct 2010, Aya Ben Yakov wrote:
Hi
I used FreeSurfer to automatically segment subcortical structures, and I
would now like to transfer the data to Matlab. I am looking for a way to load the coordinates of all structures (or, if it isn't possible, for each structure, by its number) to Matlab, in Talairach coordinates. Is this possible? If so - how can it be done?
I use BrainVoyager, not FSL, for analysis, and I would like to somehow
use the segmentation from FreeSurfer for analysis in Matlab, in combination with data I have from BrainVoyager (the functional data). I don't necessarily need talairach coordinates, but otherwise I'm not sure how it would be possible to convert between FreeSurfer and BrainVoyager.
Any suggestions? Thanks! Aya
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) (mailto:Freesurfer@nmr.mgh.harvard.edu) (mailto:Freesurfer@nmr.mgh.harvard.edu%29) https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer) (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer))
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline (http://www.partners.org/complianceline) (http://www.partners.org/complianceline (http://www.partners.org/complianceline)) . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) (mailto:Freesurfer@nmr.mgh.harvard.edu) (mailto:Freesurfer@nmr.mgh.harvard.edu%29) https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer) (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer))
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline (http://www.partners.org/complianceline) (http://www.partners.org/complianceline (http://www.partners.org/complianceline)) . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
__________________________________________________
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline (http://www.partners.org/complianceline) . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
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Aya Ben Yakov -
Bruce Fischl -
Ørjan Bergmann