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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
