I am getting an error during the recon all step that I cannot figure out. It seems to occur in the stage where labels are being written as two label files are missing in the labels directory ( lh.entorhinal_exvivo.label and lh.entorhinal_exvivo.label ) and an error log message emerges in the labels directory which says:
MRISread(/neurospin/meg/meg_ rep/anat/freesurfer_segmentation/lh.EC_average/surf/lh.sphere.reg): could not open file
In the main directory,an rh.EC_average and lh.EC_average file appears with broken links...
Does anyone know what the problem might be be. Sorry for my ignorance. Many thanks, Diana Omigie
Hi Diane
you need to symlink the directories
$FREESURFER_HOME/subjects/lh.EC_average $FREESURFER_HOME/subjects/rh.EC_average $FREESURFER_HOME/subjects/V1_average $FREESURFER_HOME/subjects/fsaverage
in your SUBJECTS_DIR
cheers Bruce
On Fri, 1 Jun 2012, Diana Omigie wrote:
I am getting an error during the recon all step that I cannot figure out. It seems to occur in the stage where labels are being written as two label files are missing in the labels directory ( lh.entorhinal_exvivo.label and lh.entorhinal_exvivo.label ) and an error log message emerges in the labels directory which says:
MRISread(/neurospin/meg/meg_rep/anat/freesurfer_segmentation/lh.EC_average/ surf/lh.sphere.reg): could not open file
In the main directory,an rh.EC_average and lh.EC_average file appears with broken links...
Does anyone know what the problem might be be. Sorry for my ignorance. Many thanks, Diana Omigie
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Diana Omigie