Hello freesurfers,
I want to select the subcortical structures (thalamus, pallidum, caudate, putamen, accumbens, hippocampus, and amygdala) and the 68 distinct brain regions as nodes of the individual brain networks. The labels are [9,11:13,17:18,26,48,50:54,58, 1002:1035, 2002:2035]. However, in the aparc+aseg.mgz files, there are also some other labels. Is there any way to delete all other unselected labels?
Thank you so much! Best,
Jinsong
Hi Jinsong
you can either copy those labels out into their own volume using mri_extract_label, or use matlab to find the other labels and zero them out
cheers Bruce
On Thu, 21 Jul 2016, Jinsong Tang wrote:
Hello freesurfers,
I want to select the subcortical structures (thalamus, pallidum, caudate, putamen, accumbens, hippocampus, and amygdala) and the 68 distinct brain regions as nodes of the individual brain networks. The labels are [9,11:13,17:18,26,48,50:54,58, 1002:1035, 2002:2035]. However, in the aparc+aseg.mgz files, there are also some other labels. Is there any way to delete all other unselected labels?
Thank you so much! Best,
Jinsong
I think you can use mri_binarize and set the match values as you like. Hope it can help.
Best,
Ismail
On Jul 21, 2016, at 2:13 PM, Jinsong Tang tangjinsonghn@gmail.com wrote:
Hello freesurfers,
I want to select the subcortical structures (thalamus, pallidum, caudate, putamen, accumbens, hippocampus, and amygdala) and the 68 distinct brain regions as nodes of the individual brain networks. The labels are [9,11:13,17:18,26,48,50:54,58, 1002:1035, 2002:2035]. However, in the aparc+aseg.mgz files, there are also some other labels. Is there any way to delete all other unselected labels?
Thank you so much! Best,
Jinsong _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
yes, that should work also On Thu, 21 Jul 2016, Koubiyr, Ismail wrote:
I think you can use mri_binarize and set the match values as you like. Hope it can help.
Best,
Ismail
On Jul 21, 2016, at 2:13 PM, Jinsong Tang tangjinsonghn@gmail.com wrote:
Hello freesurfers,
I want to select the subcortical structures (thalamus, pallidum, caudate, putamen, accumbens, hippocampus, and amygdala) and the 68 distinct brain regions as nodes of the individual brain networks. The labels are [9,11:13,17:18,26,48,50:54,58, 1002:1035, 2002:2035]. However, in the aparc+aseg.mgz files, there are also some other labels. Is there any way to delete all other unselected labels?
Thank you so much! Best,
Jinsong _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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
That will binarize all the labels, but you could then use that as a mask
On 07/21/2016 02:46 PM, Bruce Fischl wrote:
yes, that should work also On Thu, 21 Jul 2016, Koubiyr, Ismail wrote:
I think you can use mri_binarize and set the match values as you like. Hope it can help.
Best,
Ismail
On Jul 21, 2016, at 2:13 PM, Jinsong Tang tangjinsonghn@gmail.com wrote:
Hello freesurfers,
I want to select the subcortical structures (thalamus, pallidum, caudate, putamen, accumbens, hippocampus, and amygdala) and the 68 distinct brain regions as nodes of the individual brain networks. The labels are [9,11:13,17:18,26,48,50:54,58, 1002:1035, 2002:2035]. However, in the aparc+aseg.mgz files, there are also some other labels. Is there any way to delete all other unselected labels?
Thank you so much! Best,
Jinsong _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you all so much!
That's great help! I will use Matlab to delete the other labels.
Best,
Jinsong
On Thu, Jul 21, 2016 at 11:48 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
That will binarize all the labels, but you could then use that as a mask
On 07/21/2016 02:46 PM, Bruce Fischl wrote:
yes, that should work also On Thu, 21 Jul 2016, Koubiyr, Ismail wrote:
I think you can use mri_binarize and set the match values as you like. Hope it can help.
Best,
Ismail
On Jul 21, 2016, at 2:13 PM, Jinsong Tang tangjinsonghn@gmail.com
wrote:
Hello freesurfers,
I want to select the subcortical structures (thalamus, pallidum,
caudate, putamen, accumbens, hippocampus, and amygdala) and the 68 distinct brain regions as nodes of the individual brain networks. The labels are [9,11:13,17:18,26,48,50:54,58, 1002:1035, 2002:2035]. However, in the aparc+aseg.mgz files, there are also some other labels. Is there any way to delete all other unselected labels?
Thank you so much! Best,
Jinsong _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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