Weren't you concerned that the names in the annotation were incorrect? You get to pick the names and the colors to be whatever you want to be. By default, it uses FreeSurferColorLUT.txt. doug
On 6/23/12 9:54 PM, Arno Klein wrote:
dear doug,
thank you for your response. for the custom color table, what do i assign for the different anatomical names and color values? why wouldn't the names and colors in FreeSurferColorLUT.txt work?
cheers, @rno
Re: [Freesurfer] mris_label2annot mislabeling
Douglas N Greve Wed, 20 Jun 2012 08:58:50 -0700
Arno, you need to create a custom color table (--ctab). doug
On 06/20/2012 12:05 AM, Arno Klein wrote:
hello!
i have saved a couple of .label files and am trying to convert them to a .annot file with:
mris_label2annot --h lh --s MMRR-21-1 --l lh.superiorfrontal.label --l lh.superiorparietal.label --ctab FreeSurferColorLUT.txt --a output
the stdout is:
ColorTable atlas_colortable.txt AnnotName output nlables 2 LabelThresh 0 0.000000 Loading /usr/local/freesurfer/subjects/MMRR-21-1/surf/lh.orig 1 11829830 Left-Cerebral-Exterior 2 16119285 Left-Cerebral-White-Matter Mapping unhit to unknown ...clearly the anatomical names assigned are incorrect, and when i view the output with tksurfer, the labeled patches are in the right places but are assigned these same incorrect anatomical names.
i have tried renaming the .label files to no avail. what am i doing wrong?
cheers, @rno
yes, but i am confused as to how mris_label2annot uses the color table. according to http://surfer.nmr.mgh.harvard.edu/fswiki/LabelsClutsAnnotationFiles, each .label file contains columns of vertex numbers, coordinate values, and a column of zeros. i assume that mris_label2annot assigns the coordinates in the file to the anatomical name corresponding to the name of the file, but when i tried to set the color table region names to be the same as the names of the .label files, the output was the same as what i sent earlier:
1 11829830 Left-Cerebral-Exterior 2 16119285 Left-Cerebral-White-Matter ...
even though my color table didn't have label numbers 1, 2, etc.!
cheers, @rno
On Sun, Jun 24, 2012 at 11:22 AM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
Weren't you concerned that the names in the annotation were incorrect? You get to pick the names and the colors to be whatever you want to be. By default, it uses FreeSurferColorLUT.txt. doug
On 6/23/12 9:54 PM, Arno Klein wrote:
dear doug,
thank you for your response. for the custom color table, what do i assign for the different anatomical names and color values? why wouldn't the names and colors in FreeSurferColorLUT.txt work?
cheers, @rno
what was your command line? Can you send your color table? It will assign the first label to the first entry in the color table.
On 06/24/2012 11:43 AM, Arno Klein wrote:
yes, but i am confused as to how mris_label2annot uses the color table. according to http://surfer.nmr.mgh.harvard.edu/fswiki/LabelsClutsAnnotationFiles, each .label file contains columns of vertex numbers, coordinate values, and a column of zeros. i assume that mris_label2annot assigns the coordinates in the file to the anatomical name corresponding to the name of the file, but when i tried to set the color table region names to be the same as the names of the .label files, the output was the same as what i sent earlier:
1 11829830 Left-Cerebral-Exterior 2 16119285 Left-Cerebral-White-Matter ...
even though my color table didn't have label numbers 1, 2, etc.!
cheers, @rno
On Sun, Jun 24, 2012 at 11:22 AM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Weren't you concerned that the names in the annotation were incorrect? You get to pick the names and the colors to be whatever you want to be. By default, it uses FreeSurferColorLUT.txt. doug On 6/23/12 9:54 PM, Arno Klein wrote:dear doug, thank you for your response. for the custom color table, what do i assign for the different anatomical names and color values? why wouldn't the names and colors in FreeSurferColorLUT.txt work? cheers, @rno
thank you, doug! i was hung up on the names of the .label files when all that matters is the order of the labels in the lookup table. i should have figured that one out!
cheers, @rno
On Sun, Jun 24, 2012 at 3:50 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
what was your command line? Can you send your color table? It will assign the first label to the first entry in the color table.
On 06/24/2012 11:43 AM, Arno Klein wrote:
yes, but i am confused as to how mris_label2annot uses the color table. according to http://surfer.nmr.mgh.harvard.**edu/fswiki/** LabelsClutsAnnotationFileshttp://surfer.nmr.mgh.harvard.edu/fswiki/LabelsClutsAnnotationFiles, each .label file contains columns of vertex numbers, coordinate values, and a column of zeros. i assume that mris_label2annot assigns the coordinates in the file to the anatomical name corresponding to the name of the file, but when i tried to set the color table region names to be the same as the names of the .label files, the output was the same as what i sent earlier:
1 11829830 Left-Cerebral-Exterior 2 16119285 Left-Cerebral-White-Matter ...
even though my color table didn't have label numbers 1, 2, etc.!
cheers, @rno
On Sun, Jun 24, 2012 at 11:22 AM, Douglas Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>> wrote:
Weren't you concerned that the names in the annotation were incorrect? You get to pick the names and the colors to be whatever you want to be. By default, it uses FreeSurferColorLUT.txt. doug
On 6/23/12 9:54 PM, Arno Klein wrote:
dear doug,
thank you for your response. for the custom color table, what do i assign for the different anatomical names and color values? why wouldn't the names and colors in FreeSurferColorLUT.txt work?
cheers, @rno
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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