Hi,
I am trying to further script (Bash) the autorecon1 and subcortseg. The script just sets the path to the received dicom data, gets some info from the dicom header and starts the autorecon1 followed by subcortseg. The things work well when executed from the command line, but if I execute the script from another script, I get the following error during autorecon1:
mritotal -verbose -debug -clobber -modeldir /opt/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.23434/src.mnc transforms/talairach.auto.xfm Use of uninitialized value in join or string at /opt/freesurfer/mni/bin/mritotal line 462. mritotal: Couldn't find configuration file mritotal.cfg anywhere in :/opt/freesurfer/mni/bin/../etc/mni_autoreg ERROR: mritotal failed, see transforms/talairach.log
Thanks for help in advance.
Martin