search

ins-amu / scripts

prepare data for TVB
MIT License
21 stars 12 forks source link

FS v. SUBJECTS_DIR #34

Closed maedoc closed 9 years ago

maedoc commented 9 years ago

It seems that if these two environment variables do not agree, scripts does not find the results of FreeSurfer.

Why have a separate variable? I suggest either remove this from the config and expect user to set via SUBJECTS_DIR before sourcing the FreeSurfer environment or scripts should handle this itself.

timpx commented 9 years ago

Yes, I actually have in my config file export FS=$SUBJECTS_DIR. I use FS because it's shorter to write in the code, and to have a reminder for people to set $SUBJECTS_DIR. I'll move this from the configuration file to the main_surface with the appropriate warning if $SUBJECTS_DIR is not set.

timpx commented 9 years ago

see b36610e96c27ae

maedoc commented 9 years ago

ah cool; I ran into this because I was generating a config.sh from scratch and forgot to set SUBJECTS_DIR to the same value I providing for FS in the config.sh.

thanks