Hi Doug, I see. I'm trying to compare fMRI to MEG, so it would be very helpful if the same parcellation (i.e. with all 2562 labels) could be used.
How could I investigate why mris_make_face_parcellation skips a bunch of labels? The problem is not fsaverage5, because doing the analysis in native space of patients yield the same problem (and the same labels missing). So I guess exclusion of 102 labels always occurs in mris_make_face_parcellation? Thanks again, Linda On Mon, September 10, 2012 11:27 am, Douglas N Greve wrote: > > It looks like there are several (102 to be exact) that do not have any voxels in your parcellation. Eg, #82: > > 82 82 ic4.tri_vertex_82 0 > > So the problem appears to be with mris_make_face_parcellation, not with mri_segstats. > doug > > > On 09/10/2012 10:56 AM, Linda Douw wrote: >> Hi Doug, >> Output and sumfile are attached. Any ideas? >> Linda >>> Message: 10 >>> Date: Mon, 13 Aug 2012 15:55:13 -0400 >>> From: Douglas N Greve<gr...@nmr.mgh.harvard.edu> >>> Subject: Re: [Freesurfer] Freesurfer Digest, Vol 102, Issue 10 To: freesurfer@nmr.mgh.harvard.edu >>> Message-ID:<50295ba1.8090...@nmr.mgh.harvard.edu> >>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>> 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 >>>>> ------------------------------ >>>>> Message: 25 >>>>> Date: Fri, 10 Aug 2012 11:18:38 -0400 >>>>> From: Douglas N Greve<gr...@nmr.mgh.harvard.edu> >>>>> Subject: Re: [Freesurfer] ico4 parcellation and mri_segstats To: freesurfer@nmr.mgh.harvard.edu >>>>> Message-ID:<5025264e.3030...@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 > 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 > > > -- Linda Douw, Ph.D. Research fellow Department of Radiology Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School 149 13th Street Charlestown, MA 02129 _______________________________________________ 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.
