Hi Elizabeth, I'm cc'ing the list so that others may benefit from the answer:
The labels that you are referencing are defined in the aparc.a2009s atlas, but the wmparc is generated from the aparc atlas. To generate a wmparc using the a2009s, run the following: cd $SUBJECTS_DIR/subject mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.a2009s.mgz --ctxseg aparc.a2009s+aseg.mgz --a2009s Then reference wmparc.a2009s.mgz instead of wmparc.mgz in the mri_segstats cmd doug Elizabeth Gutierrez wrote: > Hi Douglas, > Thank you for directing me towards reporting form. > Here is more information: > > FREESURFER_HOME: /software/Freesurfer/5.0.0 > > Build stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 > > Debian version: squeeze/sid > > Kernel info: Linux 2.6.31-22-generic x86_64 > > 1) subject name - s120 > SUBJECTS_DIR - /mindhive/gablab/memory/sourcemem/fsdata_REM > > 2) the entire command-line executed > > *Successful -* mri_segstats --seg > /mindhive/gablab/memory/sourcemem/fsdata_REM/s120/mri/wmparc.mgz > --ctab-default --id 3001 --in fa.anat.mgh --sum fa.stats > > *Unsuccessful* - mri_segstats --seg > /mindhive/gablab/memory/sourcemem/fsdata_REM/s120/mri/wmparc.mgz > --ctab-default --id 3101 --in fa.anat.mgh --sum fa.stats > > also unsuccessful for other 30 ids from aparc2009 > -id 13112 --id 14112 --id 13113 --id 14113 --id 13114 --id 14114 --id > 13118 --id 14118 --id 13115 --id 14115 --id 13116 --id 14116 --id > 13123 --id 14123 --id 13137 --id 13138 --id 14138 --id 13148 --id > 14148 --id 13150 --id 14150 --id 13163 --id 14163 --id 13153 --id > 14153 --id 13154 --id 14154 --id 13155 --id 14155 > > > 3) the error message generated > Reporting on 0 segmentations > > > More on fa.stats file : > > > sysname Linux > # hostname ba6 > # machine x86_64 > # user eguti > # anatomy_type volume > # > # SegVolFile > /mindhive/gablab/memory/sourcemem/fsdata_REM/s120/mri/wmparc.mgz > # SegVolFileTimeStamp 2010/06/02 15:09:42 > # ColorTable /software/Freesurfer/5.0.0/FreeSurferColorLUT.txt > # ColorTableTimeStamp 2010/08/13 20:56:24 > # InVolFile fa.anat.mgh > # InVolFileTimeStamp 2010/11/05 17:09:14 > # InVolFrame 0 > # Only reporting non-empty segmentations > # VoxelVolume_mm3 1 > > > > On Wed, Nov 10, 2010 at 10:45 AM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > Hi Elizabeth, > > we'll need more info to track down the problem. Please take a look > at surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> for the > kinds of things we need. > > thanks > > doug > Elizabeth Gutierrez wrote: > > Hi, > > I've been trying to use mri_segstats on a FA map with a white > matter parcellation file (wmparc.mgz) but there might be a > problem in the program. When I open the fa.stats output file, > all the values (std.dev, etc) are 0.0000 for the 2009 table > parcellation ids. However, when I use the label id 251 (corpus > collosum) from the first few labels on the list, I get a > value. When I use the corpus collosum id for more current > labels like the aparc 2005 and 2009, I get 0.0000 again. > > Could there be a bug in the program? > > > -- > Elizabeth C. Gutierrez > Graduate Student > Department of Brain and Cognitive Sciences > Massachusetts Institute of Technology > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > 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. > > > > > -- > Elizabeth C. Gutierrez > Graduate Student > Department of Brain and Cognitive Sciences > Massachusetts Institute of Technology -- 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
