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| [wiki:Self:FreeSurferWiki top] | [[FreeSurferWiki|top]] |
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| ''' Simple Troubleshooting steps ''' [[BR]] *Check that you are using the environment you mean to be using. If you sourced an environment, you will see {{{nmr-std-env}}} or {{{nmr-dev-env}}} in your command line. Also, run {{{"which <program name>"}}} with the program you are trying to use to make sure you are using one in {{{/usr/local/freesurfer}}} or {{{/space/freesurfer}}}. *Try your command again in a new terminal. Re-source your environment, and re-type your command fully to avoid copying in prior typos. *If the failure occured with a job submitted to seychelles, try to run the job locally. |
''' Submitting a request for help ''' <<BR>> |
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| ''' Submitting a request for help ''' [[BR]] | 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. |
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| 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. [[BR]] | '''Information to include:''' * What you are trying to accomplish. * 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 (listed in the contents of your $FREESURFER_HOME/build-stamp.txt file) * Your specific platform, meaning the operating system and version you are on (e.g. Ubuntu 14.04, OSX Yosemite, etc). * If available, a copy of the recon-all.log file as an attachment to the email, found in <subject_name>/scripts/recon-all.log |
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| '''Information to Include''' *the machine you are using or your Linux distribution *environment/version you are using *your SUBJECTS_DIR *output of the {{{"which"}}} command explained above *your current working directory *the exact command line you ran *the error message you received *only report one bug at a time |
'''Example email:''' {{{ TO: freesurfer@nmr.mgh.harvard.edu FROM: fsuser@worlduniversity.edu SUBJECT: mri_segstats error: dimension mismatch between input volume and seg |
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| '''Example: see how it is done to make it easy to cut-and-paste?''' | Hello FreeSurfer Developers, |
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| on machine fishie {{{ source /usr/local/freesurfer/nmr-dev-env[[BR]] setenv SUBJECTS_DIR /space/your/subjects/dir |
I'm attempting 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 get the following error when I run the mri_segstats command: ERROR: dimension mismatch between input volume and seg input 1 1 145283 seg 145283 1 1 |
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| which mri_convert[[BR]] /usr/local/freesurfer/dev/bin//mri_convert |
I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. |
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| cd /autofs/space/blah_001/users/bert/tmp mri_convert f.mgh f.img[[BR]] reading from f.mgh...[[BR]] mghRead(/autofs/space/blah_001/users/bert/tmp/f.mgh, -1): could not open file[[BR]] |
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 |
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| ''' Where to send your questions ''' [[BR]] To get a more timely answer, it is best to send your question to a group distribution than to a specific person. There are many available depending on the nature of your problem. Please see FreeSurferSupport for more information on the available support lines. ## *the !FreeSurfer Mailing list |
See the following guide on [[http://www.catb.org/~esr/faqs/smart-questions.html|How To Ask Questions The Smart Way]] for good practices on asking questions online and increase your chances of getting a quality response. |
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:
- What you are trying to accomplish.
- 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 (listed in the contents of your $FREESURFER_HOME/build-stamp.txt file)
- Your specific platform, meaning the operating system and version you are on (e.g. Ubuntu 14.04, OSX Yosemite, etc).
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 attempting 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 get the following error when I run the mri_segstats command: ERROR: dimension mismatch between input volume and seg input 1 1 145283 seg 145283 1 1 I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, 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.