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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 commands and send us the output: | 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: |
[wiki:FreeSurferWiki top]
Bug Reporting
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
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
- 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
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:
bugr
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 /usr/local/freesurfer/nmr-dev-env
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.