Thanks for your help, Bruce!
Unfortunately, this also leads to a mgz.file where hippocampus and amygdala are "merged" together so that I can't see anymore what is hippocampus and what is amygdala (both have same value). I tried some other things but nothing appears to work. Any other suggestions?
Many thanks, Martina
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu on Thu, 24 May 2012 08:53:14 -0400 (EDT):
Hi Martina you can use mri_binarize --match 17 --match 18... to do this.
cheers Bruce
On Thu, 24 May 2012, Martina Papmeyer wrote:
Hello everyone,
I guess that this might be a simple question but I couldn't find an answer to my problem yet.
I would like to extract and visualize four labels from my aseg.mgz file for illustration purposes. I tried the following:
mri_extract_label aseg.mgz 17 18 53 54 filename.mgz
(the values correspond to left/right amygdala and left/right hippocampus as specified in FreeSurferColorLUT.txt file)
This command unfortunately combines all the four selected labels together so that I can't differentiate amygdala and hippocampus anymore when I load the filename.mgz file together with my FreeSurferColorLUT.txt file in tkmedit.
Is there any other FS tool I can use?
Any form of help would be highly appreciated!
Many thanks and all best wishes, Martina
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 Martina, what exactly do you want? You can get a separate file for each seg with different calls to mri_binarize specifying only one label. doug
On 05/24/2012 10:38 AM, Martina Papmeyer wrote:
Thanks for your help, Bruce!
Unfortunately, this also leads to a mgz.file where hippocampus and amygdala are "merged" together so that I can't see anymore what is hippocampus and what is amygdala (both have same value). I tried some other things but nothing appears to work. Any other suggestions?
Many thanks, Martina
Quoting Bruce Fischlfischl@nmr.mgh.harvard.edu on Thu, 24 May 2012 08:53:14 -0400 (EDT):
Hi Martina you can use mri_binarize --match 17 --match 18... to do this.
cheers Bruce
On Thu, 24 May 2012, Martina Papmeyer wrote:
Hello everyone,
I guess that this might be a simple question but I couldn't find an answer to my problem yet.
I would like to extract and visualize four labels from my aseg.mgz file for illustration purposes. I tried the following:
mri_extract_label aseg.mgz 17 18 53 54 filename.mgz
(the values correspond to left/right amygdala and left/right hippocampus as specified in FreeSurferColorLUT.txt file)
This command unfortunately combines all the four selected labels together so that I can't differentiate amygdala and hippocampus anymore when I load the filename.mgz file together with my FreeSurferColorLUT.txt file in tkmedit.
Is there any other FS tool I can use?
Any form of help would be highly appreciated!
Many thanks and all best wishes, Martina
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 Doug,
thanks for your help. I need a file with four segmentations being displayed (as outlined below: left/right amygdala and left/right hippocampus). I know how to just display ONE segmentation using mri_binarize or mri_extract_label. However, I need to display ALL of the four and all should have different values (colours) so that you can differentiate them well from each other.
All best, Martina
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu on Thu, 24 May 2012 10:40:17 -0400:
Hi Martina, what exactly do you want? You can get a separate file for each seg with different calls to mri_binarize specifying only one label. doug
On 05/24/2012 10:38 AM, Martina Papmeyer wrote:
Thanks for your help, Bruce!
Unfortunately, this also leads to a mgz.file where hippocampus and amygdala are "merged" together so that I can't see anymore what is hippocampus and what is amygdala (both have same value). I tried some other things but nothing appears to work. Any other suggestions?
Many thanks, Martina
Quoting Bruce Fischlfischl@nmr.mgh.harvard.edu on Thu, 24 May 2012 08:53:14 -0400 (EDT):
Hi Martina you can use mri_binarize --match 17 --match 18... to do this.
cheers Bruce
On Thu, 24 May 2012, Martina Papmeyer wrote:
Hello everyone,
I guess that this might be a simple question but I couldn't find an answer to my problem yet.
I would like to extract and visualize four labels from my aseg.mgz file for illustration purposes. I tried the following:
mri_extract_label aseg.mgz 17 18 53 54 filename.mgz
(the values correspond to left/right amygdala and left/right hippocampus as specified in FreeSurferColorLUT.txt file)
This command unfortunately combines all the four selected labels together so that I can't differentiate amygdala and hippocampus anymore when I load the filename.mgz file together with my FreeSurferColorLUT.txt file in tkmedit.
Is there any other FS tool I can use?
Any form of help would be highly appreciated!
Many thanks and all best wishes, Martina
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.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
In that case, use mri_binarize to get a mask of all the segmentations you want to display, then run mri_mask, something like
mri_mask aseg.mgz mask.mgz aseg-masked.mgz
doug
On 05/24/2012 10:45 AM, Martina Papmeyer wrote:
Hi Doug,
thanks for your help. I need a file with four segmentations being displayed (as outlined below: left/right amygdala and left/right hippocampus). I know how to just display ONE segmentation using mri_binarize or mri_extract_label. However, I need to display ALL of the four and all should have different values (colours) so that you can differentiate them well from each other.
All best, Martina
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu on Thu, 24 May 2012 10:40:17 -0400:
Hi Martina, what exactly do you want? You can get a separate file for each seg with different calls to mri_binarize specifying only one label. doug
On 05/24/2012 10:38 AM, Martina Papmeyer wrote:
Thanks for your help, Bruce!
Unfortunately, this also leads to a mgz.file where hippocampus and amygdala are "merged" together so that I can't see anymore what is hippocampus and what is amygdala (both have same value). I tried some other things but nothing appears to work. Any other suggestions?
Many thanks, Martina
Quoting Bruce Fischlfischl@nmr.mgh.harvard.edu on Thu, 24 May 2012 08:53:14 -0400 (EDT):
Hi Martina you can use mri_binarize --match 17 --match 18... to do this.
cheers Bruce
On Thu, 24 May 2012, Martina Papmeyer wrote:
Hello everyone,
I guess that this might be a simple question but I couldn't find an answer to my problem yet.
I would like to extract and visualize four labels from my aseg.mgz file for illustration purposes. I tried the following:
mri_extract_label aseg.mgz 17 18 53 54 filename.mgz
(the values correspond to left/right amygdala and left/right hippocampus as specified in FreeSurferColorLUT.txt file)
This command unfortunately combines all the four selected labels together so that I can't differentiate amygdala and hippocampus anymore when I load the filename.mgz file together with my FreeSurferColorLUT.txt file in tkmedit.
Is there any other FS tool I can use?
Any form of help would be highly appreciated!
Many thanks and all best wishes, Martina
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.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
amazing! It works - thanks a million :) Martina
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu on Thu, 24 May 2012 10:56:18 -0400:
In that case, use mri_binarize to get a mask of all the segmentations you want to display, then run mri_mask, something like
mri_mask aseg.mgz mask.mgz aseg-masked.mgz
doug
On 05/24/2012 10:45 AM, Martina Papmeyer wrote:
Hi Doug,
thanks for your help. I need a file with four segmentations being displayed (as outlined below: left/right amygdala and left/right hippocampus). I know how to just display ONE segmentation using mri_binarize or mri_extract_label. However, I need to display ALL of the four and all should have different values (colours) so that you can differentiate them well from each other.
All best, Martina
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu on Thu, 24 May 2012 10:40:17 -0400:
Hi Martina, what exactly do you want? You can get a separate file for each seg with different calls to mri_binarize specifying only one label. doug
On 05/24/2012 10:38 AM, Martina Papmeyer wrote:
Thanks for your help, Bruce!
Unfortunately, this also leads to a mgz.file where hippocampus and amygdala are "merged" together so that I can't see anymore what is hippocampus and what is amygdala (both have same value). I tried some other things but nothing appears to work. Any other suggestions?
Many thanks, Martina
Quoting Bruce Fischlfischl@nmr.mgh.harvard.edu on Thu, 24 May 2012 08:53:14 -0400 (EDT):
Hi Martina you can use mri_binarize --match 17 --match 18... to do this.
cheers Bruce
On Thu, 24 May 2012, Martina Papmeyer wrote:
Hello everyone,
I guess that this might be a simple question but I couldn't find an answer to my problem yet.
I would like to extract and visualize four labels from my aseg.mgz file for illustration purposes. I tried the following:
mri_extract_label aseg.mgz 17 18 53 54 filename.mgz
(the values correspond to left/right amygdala and left/right hippocampus as specified in FreeSurferColorLUT.txt file)
This command unfortunately combines all the four selected labels together so that I can't differentiate amygdala and hippocampus anymore when I load the filename.mgz file together with my FreeSurferColorLUT.txt file in tkmedit.
Is there any other FS tool I can use?
Any form of help would be highly appreciated!
Many thanks and all best wishes, Martina
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.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Martina Papmeyer