Hi,

I apologize for spamming the list, but for future reference this problem was resolved when I opened the color table and annotation file on the average brain in tksurfer and then exported the annotation file with a new name. Using the new annotation file with mri_surfcluster, the color table was read in correctly and the labels were generated in the cluster table.

Cheers, Elisa

On Wed, May 11, 2011 at 1:02 PM, Elisa Golfinopoulos egolfino@bu.eduwrote:

Hi all,

I wanted to follow-up on my previous e-mail, which may have been a bit too vague.

I am using the command:

mri_surfcluster --in ./osgm/sig.mgh --subject average --surf inflated --annot slt --sign abs --csd ../csd/mc-z.abs-osgm.csd --sum ./osgm/summaryfile.txt --o ./osgm/cluster_peaks.o --ocn ./osgm/cluster_number.ocn --sd /speechlab/2/egolfino/srate/nipype/fsdata

This command runs without error. The slt annotation file is found in the right directory and read, but when I display the summary text file I find that for each cluster the label under Annot is "NOT FOUND."

This is not the case when I use mri_surfcluster, but substitute slt with aparc. That is, when I use this substitution, in the summary text file under Annot Freesurfer's labels are generated.

I notice that when I run mri_surfcluster with aparc, after the annotation file is read, the colortable is read from the annotation file and the terminal indicates "colortables with 36 entries read (originally /autofs/space/terrer_001/users/nicks/freesurfer/average/colortable_desikan_killany.txt)." The color table is not read when I run mri_surfcluster with the slt annotation file.

I am assuming that our slt annotation file is missing information in the header regarding the corresponding color table and I am wondering if there is a way for me to generate a link between the annotation file and the color table? Is it possible for me to set the color table information in the annotation file or set the color table information externally so mri_surfcluster knows which label corresponds with each id?

Any suggestions would be greatly appreciated.

Thanks so much for your help.

Cheers, Elisa

P.S.: I am using the 5th version of Freesurfer for a 64 bit machine.

On Mon, May 2, 2011 at 5:33 PM, Elisa Golfinopoulos egolfino@bu.eduwrote:

...

Hi,

I am trying to use an annotation file that was created from a parcellation scheme developed in my lab with mri_surfcluster. However, it's unclear to me how I can set the corresponding color table for this annotation file either locally or globally. mri_surfcluster doesn't seem to have a --ctab or --colortable argument. Is there a way to set the color table as an environment variable and would this be an appropriate workaround or is it the case that the color table is a fixed setting for mri_surfcluster?

Your help is greatly appreciated.

Cheers, Elisa

-- Elisa Golfinopoulos Speech Laboratory Cognitive and Neural Systems Boston University Phone: 617.353.6181

-- Elisa Golfinopoulos Speech Laboratory Cognitive and Neural Systems Boston University Phone: 617.353.6181