Bug Reporting

Simple Troubleshooting steps

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

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

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

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.