| Deletions are marked like this. | Additions are marked like this. |
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| *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}}}. | *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}}}. |
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| ''Information to Include'' | '''Information to Include''' |
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| *output of the {{{which}}} command explained above |
*your SUBJECTS_DIR *output of the {{{"which"}}} command explained above |
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| *your SUBJECTS_DIR | |
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'''Example: see how it is done to make it easy to cut-and-paste?''' source /usr/local/freesurfer/nmr-dev-env[[BR]] setenv SUBJECTS_DIR /space/your/subjects/dir which mri_convert[[BR]] /usr/local/freesurfer/dev/bin//mri_convert 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]] |
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. We need to be able to open a new shell and go from there to 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
- 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
Example: see how it is done to make it easy to cut-and-paste?
source /usr/local/freesurfer/nmr-dev-envBR setenv SUBJECTS_DIR /space/your/subjects/dir
which mri_convertBR /usr/local/freesurfer/dev/bin//mri_convert
cd /autofs/space/blah_001/users/bert/tmp
mri_convert f.mgh f.imgBR
reading from f.mgh...BR mghRead(/autofs/space/blah_001/users/bert/tmp/f.mgh, -1): could not open fileBR
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.