Hi Linda, can you send the terminal output for mri_segstats? Can you also send the summary file? doug

On 08/13/2012 10:59 AM, Linda Douw wrote:

Hi Doug,

I first parcellate fsaverage5 using ico4 (all my functional data are morphed to fsaverage5 surface):

mris_make_face_parcellation /fsaverage5/rh.inflated $FREESURFER_HOME/lib/bem/ic4.tri rh.ico4.annot

Then I extract the waveforms using mri_segstats

mri_segstats --i rh.functional.nii.gz --avgwf rh_ico4.txt --annot fsaverage5c rh ico4 --sum ico4_rh.sum

Hope this clarifies the problem! Linda

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Message: 25 Date: Fri, 10 Aug 2012 11:18:38 -0400 From: Douglas N Grevegreve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ico4 parcellation and mri_segstats To: freesurfer@nmr.mgh.harvard.edu Message-ID:5025264E.3030801@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed

what are your command lines? doug

On 08/09/2012 01:21 PM, Linda Douw wrote:

...

Dear Freesurfers,

I'm trying to extract the average waveforms from all 2562 ROIs in an annotation constructed using mris_make_face_parcellation with ico4. However, I get only 2460 waveforms after doing mri_segstats, and the summary files show that several ROIs are 'skipped' for some reason. Am I missing something?

Thanks,

-- 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

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