Hi Tudor, you can create a symbolic link to fsaverage rather than copying it. doug
On 12/14/2012 04:18 PM, Tudor Popescu wrote:
Hello everyone,
I'm following the group analysis tutorial, but have difficulty getting all files in the right folders. I have my tutorial data set in //media/Dell/_FS/buckner_data// (a folder that is shared in my VirtualBox), and my original subjects folder in the default path of //home/virtualuser/freesurfer/subjects/.
The tutorial page http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data suggests that the data set should be inside /$FREESURFER_HOME/subjects/, however I have no room in my virtual drive to copy over the whole data set, and VirtualBox is making it difficult for me to extend its size. I have thus defined SUBJECTS_DIR to be//media/Dell/_FS/buckner_data//, but then the first command of the analysis (mris_preproc) says it can't find fsaverage!
The command only works if I create a new folder and copy the following in there:
- the contents of //group_analysis_tutorial/ (i.e. folders of the type /004/, /008/, ..), and
- the contents of//home/virtualuser/freesurfer/subjects/ (i.e. folders such as /bert/, /fsaverage/, ..)
..and then run the command from there -- however, this seems very cumbersome and takes a lot of time.
My question: does one always have to copy the fsaverage folder manually at the same level as the data folders, or does it have to be the other way around (i.e. data set copied into default //subjects/ folder)? Can't there be two environment variables, one for fsaverages and one for the data set, so that no moving/copying is necessary?
Many thanks for any help! Tudor
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