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