Hi Vanessa, Is sparseg a directory? Try pointing it at one of the dcm files from that set . Best Martin

On May 12, 2011, at 8:21 PM, Vanessa Lim v.lim@auckland.ac.nz wrote:

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

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