Hi I tried running the following process. Convert aseg.mgz back to native space using: mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg_nat.mgz --regheader aseg.mgz Then I loaded the aseg_nat (which, to my understanding, should be in native space) to matlab. Now mri.vol (using MRIread) has data 256X256X176, the same dimensions as the original data However, when I convert to nii, and then to brainvoyager format, there's a rotation (perhaps also distortion, but I couldn't see with the rotation), the dimensions don't match (sagittal appears in coronal etc.). When I try to flip the two 256 dimensions, it doesn't help, which means somehow the 176 dimension and the 256 dimension got flipped in the process. If anyone has an idea how to solve this it would be very helpful.
Thanks, Aya
__________________________________________________
From Aya Ben Yakov ayab@mail.weizmann.ac.il
Sent Wed 10/27/2010 3:04 PM To Bruce Fischl fischl@nmr.mgh.harvard.edu Cc freesurfer@nmr.mgh.harvard.edu Subject Re: [Freesurfer] subcortical structure coordinates
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
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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 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.
How are you converting to nifti? You can do it with mri_label2vol, just spec nii instead of mgz.
doug
Aya Ben Yakov wrote:
Hi I tried running the following process. Convert aseg.mgz back to native space using: mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg_nat.mgz --regheader aseg.mgz Then I loaded the aseg_nat (which, to my understanding, should be in native space) to matlab. Now mri.vol (using MRIread) has data 256X256X176, the same dimensions as the original data However, when I convert to nii, and then to brainvoyager format, there's a rotation (perhaps also distortion, but I couldn't see with the rotation), the dimensions don't match (sagittal appears in coronal etc.). When I try to flip the two 256 dimensions, it doesn't help, which means somehow the 176 dimension and the 256 dimension got flipped in the process. If anyone has an idea how to solve this it would be very helpful.
Thanks, Aya
From Aya Ben Yakov ayab@mail.weizmann.ac.il Sent Wed 10/27/2010 3:04 PM To Bruce Fischl fischl@nmr.mgh.harvard.edu Cc freesurfer@nmr.mgh.harvard.edu Subject Re: [Freesurfer] subcortical structure coordinates
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
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
At first I tried converting to nifti in matlab, using MRIWrite, which resulted in permuted dimensions. When I tried creating the nii file directly, I got the same values in the vol matrix.
I thought that perhaps it would be possible to run the recon on a file converted from nii (from an anatomical file), not from the original dicoms. Is this possible? I'm not sure what the difference is between T1.mgz and brainmask.mgz created when first reading the subject's dicoms - can I just take a nii file, save it as one of those files, and then run the recon-all, or is there an additional step?
Thanks! Aya
-----Original Message-----
From Douglas N Greve greve@nmr.mgh.harvard.edu
Sent Thu 10/28/2010 7:43 PM To Aya Ben Yakov aya.benyakov@weizmann.ac.il Cc freesurfer@nmr.mgh.harvard.edu Subject Re: [Freesurfer] subcortical structure coordinates
How are you converting to nifti? You can do it with mri_label2vol, just spec nii instead of mgz.
doug
Aya Ben Yakov wrote:
Hi I tried running the following process. Convert aseg.mgz back to native space using: mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg_nat.mgz --regheader aseg.mgz Then I loaded the aseg_nat (which, to my understanding, should be in native space) to matlab. Now mri.vol (using MRIread) has data 256X256X176, the same dimensions as the original data However, when I convert to nii, and then to brainvoyager format, there's a rotation (perhaps also distortion, but I couldn't see with the rotation), the dimensions don't match (sagittal appears in coronal etc.). When I try to flip the two 256 dimensions, it doesn't help, which means somehow the 176 dimension and the 256 dimension got flipped in the process. If anyone has an idea how to solve this it would be very helpful.
Thanks, Aya
From Aya Ben Yakov ayab@mail.weizmann.ac.il Sent Wed 10/27/2010 3:04 PM To Bruce Fischl fischl@nmr.mgh.harvard.edu Cc freesurfer@nmr.mgh.harvard.edu Subject Re: [Freesurfer] subcortical structure coordinates
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
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Aya Ben Yakov -
Douglas N Greve