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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. |
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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>> | 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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'''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 |
'''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 () * 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 |
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'''New in v3.0.4:''' A script called '''bugr''' will gather most of this information and remind you of the other information to gather. At the command line, type: |
'''Example email:''' |
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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 |
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If you do not have that script, then follow this example. Let's say your problem is with mri_convert, you would type these example commands and send us the output: {{{ uname -a cat $FREESURFER_HOME/build-stamp.txt source $FREESURFER_HOME/SetUpFreeSurfer.csh }}} and then you might give us some details on exactly what subject (if at the NMR Center) and command was used: {{{ setenv SUBJECTS_DIR /space/your/subjects/dir which mri_convert cd /autofs/space/blah_001/users/bert/tmp mri_convert f.mgh f.img }}} and whatever you send us should reproduce the error, in this case, something like: {{{ ... mri_convert f.mgh f.img reading from f.mgh... mghRead(/autofs/space/blah_001/users/bert/tmp/f.mgh, -1): could not open file }}} ''' 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:
- 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 ()
- 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.