Dear Experts, I've made some volumes from aseg.mgz using mri_binarize and then used mri_convert to make nii files. But when i open these files using Mricro i see the original dimension of the image has changed ( 181,217,181 to 256,256,256). I have no idea what the problem is. I'd appreciate your help. Many thanks in advance Best
all of our data is transformed to be 256^3 before processing unless you specify otherwise. If you want to undo it, you can use the -rl <volume name> switch in mri_convert ("reslice like"). If it is an aseg volume make sure that you specify the resample type as nearest neighbor with -rt nearest
Note also that all of our binaries can write nifti (including mri_binarize) cheers Bruce
On Wed, 4 Oct 2017, Fereshte wrote:
Dear Experts,I've made some volumes from aseg.mgz using mri_binarize and then used mri_convert to make nii files. But when i open these files using Mricro i see the original dimension of the image has changed ( 181,217,181 to 256,256,256). I have no idea what the problem is. I'd appreciate your help. Many thanks in advance Best
This is a standard operation in FS to change the volume to 256^3, 1mm^3. If you need to get the data back into the native space, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On 10/4/17 3:31 AM, Fereshte wrote:
Dear Experts, I've made some volumes from aseg.mgz using mri_binarize and then used mri_convert to make nii files. But when i open these files using Mricro i see the original dimension of the image has changed ( 181,217,181 to 256,256,256). I have no idea what the problem is. I'd appreciate your help. Many thanks in advance Best
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Dear Experts, I've run " mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz" as explained, however i can't see any changes in dimension in comparision to the the predefined aseg.mgz. I'd appreciate your help with it. Thanks for your attention. I'm looking forward to your reply.
On Wed, Oct 4, 2017 at 5:01 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
This is a standard operation in FS to change the volume to 256^3, 1mm^3. If you need to get the data back into the native space, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On 10/4/17 3:31 AM, Fereshte wrote:
Dear Experts, I've made some volumes from aseg.mgz using mri_binarize and then used mri_convert to make nii files. But when i open these files using Mricro i see the original dimension of the image has changed ( 181,217,181 to 256,256,256). I have no idea what the problem is. I'd appreciate your help. Many thanks in advance Best
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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I found out the problem, thank you. Cheers On Sun, Oct 8, 2017 at 9:21 AM Fereshte fereshte.ramezani@gmail.com wrote:
Dear Experts, I've run " mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz" as explained, however i can't see any changes in dimension in comparision to the the predefined aseg.mgz. I'd appreciate your help with it. Thanks for your attention. I'm looking forward to your reply.
On Wed, Oct 4, 2017 at 5:01 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
This is a standard operation in FS to change the volume to 256^3, 1mm^3. If you need to get the data back into the native space, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On 10/4/17 3:31 AM, Fereshte wrote:
Dear Experts, I've made some volumes from aseg.mgz using mri_binarize and then used mri_convert to make nii files. But when i open these files using Mricro i see the original dimension of the image has changed ( 181,217,181 to 256,256,256). I have no idea what the problem is. I'd appreciate your help. Many thanks in advance Best
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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
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.
what is the dimension of the rawavg.mgz? what is the dimension of the output? What is the terminal output?
On 10/8/17 1:51 AM, Fereshte wrote:
Dear Experts, I've run " mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz" as explained, however i can't see any changes in dimension in comparision to the the predefined aseg.mgz. I'd appreciate your help with it. Thanks for your attention. I'm looking forward to your reply.
On Wed, Oct 4, 2017 at 5:01 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
This is a standard operation in FS to change the volume to 256^3, 1mm^3. If you need to get the data back into the native space, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat <https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat> On 10/4/17 3:31 AM, Fereshte wrote:Dear Experts, I've made some volumes from aseg.mgz using mri_binarize and then used mri_convert to make nii files. But when i open these files using Mricro i see the original dimension of the image has changed ( 181,217,181 to 256,256,256). I have no idea what the problem is. I'd appreciate your help. Many thanks in advance Best _______________________________________________ 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>_______________________________________________ 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.
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I found out the problem, thanks for your attention. Regards
On Tue, Oct 10, 2017 at 12:32 AM Douglas Greve greve@nmr.mgh.harvard.edu wrote:
what is the dimension of the rawavg.mgz? what is the dimension of the output? What is the terminal output?
On 10/8/17 1:51 AM, Fereshte wrote:
Dear Experts, I've run " mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz" as explained, however i can't see any changes in dimension in comparision to the the predefined aseg.mgz. I'd appreciate your help with it. Thanks for your attention. I'm looking forward to your reply.
On Wed, Oct 4, 2017 at 5:01 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
This is a standard operation in FS to change the volume to 256^3, 1mm^3. If you need to get the data back into the native space, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On 10/4/17 3:31 AM, Fereshte wrote:
Dear Experts, I've made some volumes from aseg.mgz using mri_binarize and then used mri_convert to make nii files. But when i open these files using Mricro i see the original dimension of the image has changed ( 181,217,181 to 256,256,256). I have no idea what the problem is. I'd appreciate your help. Many thanks in advance Best
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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
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 listFreesurfer@nmr.mgh.harvard.eduhttps://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
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@nmr.mgh.harvard.edu
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Douglas Greve -
Fereshte