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