Hi,

 

I have files from Siemen's Skyra which I have used MRI_Convert to nii

I have tried using just the dicom files as well as changing the files to *.nii.gz but I still get the error

corRead(): can't open file /home/virtualuser/apps/freesurfer/subjects/SPARSEG/COR-.info
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $

I get files in G2 but there is nothing in the mri/orig

I am following http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction

as I am completely new to freesurfer.  I'm using a virtual machine on Vista; Ubantu.

 

Many thanks!

Regards,

Vanessa

 

Error below:

FreeSurfer:~/apps/freesurfer/subjects/GrossNii> recon-all -i ~/apps/freesurfer/subjects/SPARSEG -subjid G2
Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.0.0
Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.0.0
INFO: SUBJECTS_DIR is /home/virtualuser/apps/freesurfer/subjects
Actual FREESURFER_HOME /home/virtualuser/apps/freesurfer
Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux
/home/virtualuser/apps/freesurfer/subjects/G2

 mri_convert /home/virtualuser/apps/freesurfer/subjects/SPARSEG /home/virtualuser/apps/freesurfer/subjects/G2/mri/orig/001.mgz

mri_convert /home/virtualuser/apps/freesurfer/subjects/SPARSEG /home/virtualuser/apps/freesurfer/subjects/G2/mri/orig/001.mgz
corRead(): can't open file /home/virtualuser/apps/freesurfer/subjects/SPARSEG/COR-.info
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from /home/virtualuser/apps/freesurfer/subjects/SPARSEG...
Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux