Hi Elisa, how was the slt file created? Can you send it and the summary file to me (don't send to the group). doug
Elisa Golfinopoulos wrote: > 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 <egolf...@bu.edu > <mailto:egolf...@bu.edu>> wrote: > > 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 <tel:617.353.6181> > > > > > -- > Elisa Golfinopoulos > Speech Laboratory > Cognitive and Neural Systems > Boston University > Phone: 617.353.6181 <tel:617.353.6181> > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 gr...@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 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.
