On 12/14/2012 04:51 PM, Tudor Popescu wrote: > Thanks Doug! I tried figuring out how to create symlinks manually (as > I think recon-all has already been run in the case of the group > analysis tutorial, therefore they were not generated automatically) > but could not find anything helpful on the wiki. cd $SUBJECTS_DIR ln -s $FREESURFER_HOME/fsaverage > > I also looked for a tutorial on how to run recon-all on raw NIFTI > files (which I guess first have to be converted to MGZ), as I'd first > have to do this step to my own data before starting to follow the > steps described in the group analysis tutorial. You can just spec the nifti file as input (--i file.nii), you do not need to convert doug > > Tudor > > On 14 December 2012 21:23, Douglas N Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > Hi Tudor, you can create a symbolic link to fsaverage rather than > copying it. > doug > > > On 12/14/2012 04:18 PM, Tudor Popescu wrote: > > Hello everyone, > > > > I'm following the group analysis tutorial, but have difficulty > getting > > all files in the right folders. I have my tutorial data set in > > //media/Dell/_FS/buckner_data// (a folder that is shared in my > > VirtualBox), and my original subjects folder in the default path of > > //home/virtualuser/freesurfer/subjects/. > > > > The tutorial page > > <http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data> suggests > > that the data set should be inside /$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 > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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 <mailto: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. > >
-- 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
