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Bug Reporting

Submitting a request for help

When submitting a request for help with your problems please be aware that the developers will try and repeat your error in order to fix it. They need to be able to go from opening a new shell to reproducing your error message. To help them be most efficient, please be sure to include the following information in an easy-to-read, cut-and-paste format.

Information to include:

• A detailed description of the problem and any attempts, if any, you made at solving it.
• The command you are trying to run (e.g. recon-all) and the exact error output to the screen.

• The version of FreeSurfer you are using, found in the $FREESURFER_HOME/build-stamp.txt file (e.g. freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0)

• The operating system and version you are on (e.g. Ubuntu 14.04, OS X Yosemite, etc).

• Output of the uname -a command.

• If available, a copy of the recon-all.log file as an attachment to the email, found in <subject_name>/scripts/recon-all.log

Example email:

TO: freesurfer@nmr.mgh.harvard.edu
FROM: fsuser@worlduniversity.edu
SUBJECT: mri_segstats error: dimension mismatch between input volume and seg

Hello FreeSurfer Developers,

I'm atempting to compute average contrast in anatomical ROIs constrained by functional activation, as described on the MultiModal FMRI tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriIndividual_freeview), but for some of my subjects I'm getting the following errors that when I run the mri_segstats command. Ive searched the list and no similar errors have been reported.
 
  ERROR: dimension mismatch between input volume and seg
  input 1 1 145283
  seg   145283 1 1

Does anyone have any thoughts on how to trouble-shoot this one? Ive attached the recon-all.log in case it's of any use. 

1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
2) Platform: CentOS release 6.7 (Final)
3) uname -a: Linux sand 2.6.32-573.3.1.el6.x86_64 #1 SMP Thu Aug 13 22:55:16 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
4) recon-all.log: see attached

See the following guide on How To Ask Questions The Smart Way for good practices on asking questions online and increase your chances of getting a quality response.