Dear List,

 

when I try to use bbregister it gives out an ERROR saying it can't find the subject.

 

I use freesurfer on a server where it is installed for everybody to use, but i'm not allowed to write in the subject_dir in this home-directory (e.g. "apps/freesurfer/subjects". Therefor I want to tell via command line where to find the subject and where to put the output data.

 

bbregister --s $SUBJ_DIR --mov $TEMP_DIR --reg registration.reg --init-rr --t1 --o $OUT_DIR

 

when I try it like this, freesurfer seems to look for the path given in $SUBJ_DIR in the homedirectory "apps/freesurfer/subjects", which doesn't make sense at all...

Can anybody help me with this problem?

Thanks a lot! M