Hi, I'm a beginner of freesurfer, I was going through the tutorial step by step in Linux. After 'export FREESURFER_HOME=/usr/local/freesurfer' 1) 'source $FREESURFER_HOME/SetUpFreeSurfer.sh' the interface showed: FREESURFER_HOME /home/aimsl/freesurfer FSFAST_HOME /home/aimsl/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /home/aimsl/freesurfer/subjects INFO: /home/aimsl/matlab/startup.m does not exist...creating touch: cannot touch '/home/aimsl/matlab/startup.m': Permission denied bash: /home/aimsl/matlab/startup.m: Permission denied ... (same with top) ... (same with top) MNI_DIR /home/aimsl/freesurfer/mni
2) cp $FREESURFER_HOME/subjects/sample-001.mgz . mri_convert sample-001.mgz sample-001.nii.gz this step showed same output with that showed in freesurfer website ... reading from sample-001.mgz... TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to sample-001.nii.gz... 3)recon-all -i sample-001.nii.gz -s bert -all it showed: bash: /home/aimsl/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such file or directory
Thanks in advance!
Best Xiao