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 <greve@nmr.mgh.harvard.edu mailto:greve@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
greve@nmr.mgh.harvard.edu <mailto:greve@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.