Hi all
I am using freesurfer 4.5.0 and i get the following message after i execute
recon-all -s 10272009 -autorecon-all
#@# Nu Intensity Correction Tue Jan 26 08:18:31 EST 2010
mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 opening /usr/local/freesurfer-4.5.0/FreeSurferEnv.ninds Setting=up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME=/usr/local/freesurfer-4.5.0 FSFAST_HOME=/usr/local/freesurfer-4.5.0/fsfast FSF_OUTPUT_FORMAT=nii SUBJECTS_DIR=/home/evangeloui/freesurfer/subjects MNI_DIR=/usr/local/freesurfer-4.5.0/mni FSL_DIR=/usr/local/fsl
opening /usr/local/freesurfer-4.5.0/FreeSurferEnv.ninds Setting=up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME=/usr/local/freesurfer-4.5.0 FSFAST_HOME=/usr/local/freesurfer-4.5.0/fsfast FSF_OUTPUT_FORMAT=nii SUBJECTS_DIR=/home/evangeloui/freesurfer/subjects MNI_DIR=/usr/local/freesurfer-4.5.0/mni FSL_DIR=/usr/local/fsl ERROR: flag opening not recognized #-------------------------------------------- #@# Talairach Tue Jan 26 08:18:31 EST 2010 /home/evangeloui/freesurfer/subjects/10272009/mri
talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm opening /usr/local/freesurfer-4.5.0/FreeSurferEnv.ninds Setting=up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME=/usr/local/freesurfer-4.5.0 FSFAST_HOME=/usr/local/freesurfer-4.5.0/fsfast FSF_OUTPUT_FORMAT=nii SUBJECTS_DIR=/home/evangeloui/freesurfer/subjects MNI_DIR=/usr/local/freesurfer-4.5.0/mni FSL_DIR=/usr/local/fsl
opening /usr/local/freesurfer-4.5.0/FreeSurferEnv.ninds Setting=up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME=/usr/local/freesurfer-4.5.0 FSFAST_HOME=/usr/local/freesurfer-4.5.0/fsfast FSF_OUTPUT_FORMAT=nii SUBJECTS_DIR=/home/evangeloui/freesurfer/subjects MNI_DIR=/usr/local/freesurfer-4.5.0/mni FSL_DIR=/usr/local/fsl ERROR: flag opening not recognized
cp transforms/talairach.auto.xfm transforms/talairach.xfm
cp: cannot stat `transforms/talairach.auto.xfm': No such file or directory
any help would be appreciated
thanks
------------------------------------------------------------------- Iordanis E. Evangelou, DPhil Staff Scientist Neuroimmunology Branch National Institute of Neurological Disorders and Stroke National Institutes of Health Building 10, Room 5C203B Bethesda, MD 20892