Hi Ana, this looks like the "getrunlist" error that we've encountered on the mac (nothing to do with philips). To fix this, download:

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/getrunlist cp getrunlist $FREESURFER_HOME/fsfast/bin

and it should work

doug

ana ;osp wrote:

Hello all-

We are trying to do preprocessing on data collected with a Philips scanner. We could not make unpacking step work. Instead, we converted the dcm files for a run of interest using mri_convert and created a nifti file. We placed this file under Applications/freesurfer/sessions/<project>/<subject>/bold/001 directory.

So when we run preproc-sess -s < subject > -fwhm 5 We get: ERROR: You must specify -per-run or -per-session

When we run preproc-sess -s < subject > -fwhm 5 -per-run We get:

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preproc-sess logfile is log/preproc-sess.log

$Id: preproc-sess,v 1.31.2.4 2010/07/26 15:55:24 greve Exp $

setenv FREESURFER_HOME /Applications/freesurfer setenv SUBJECTS_DIR /Applications/freesurfer/subjects

/Applications/freesurfer/sessions/< project > /Applications/freesurfer/fsfast/bin/preproc-sess -s < subject > -fwhm 5 -per-run Wed Apr 20 16:10:32 EDT 2011 instem f mc 1 f fmcpr stc 0 fmcpr sm 0 mask 1 brain <subject> Template ----------------------------- mktemplate-sess -s < subject > -d /Applications/freesurfer/sessions/<project> -fsd bold -update

Session: /Applications/freesurfer/sessions/< project >/< subject >

Wed Apr 20 16:10:32 EDT 2011 find: illegal option -- m find: illegal option -- a find: illegal option -- e find: illegal option -- p find: illegal option -- t find: illegal option -- h find: 1: No such file or directory ERROR: no run directories found

Does anyone know how to fix this problem?

Thank you very much

Ana

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