Hello,
I still new in using freesurfer.
the freesurfer was successfully installed.
but when i tried to run recon-all it give an error.
[Ainis-iMac:~] ismafairus% setenv FREESURFER_HOME Applications/freesurfer
[Ainis-iMac:~] ismafairus% source $FREESURFER_HOME/SetUpFreeSurfer.csh
-------- freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME Applications/freesurfer
FSFAST_HOME Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR Applications/freesurfer/subjects
MNI_DIR Applications/freesurfer/mni
FSL_DIR FSL/fsl
Ainis-iMac:~] ismafairus% recon-all -i $SUBJECTS_DIR/us03.nii.gz -o us03 -all
ERROR: cannot find Applications/freesurfer/subjects/us03.nii.gz
Darwin Ainis-iMac.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18
12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64
recon-all -s exited with ERRORS at Sat Dec 1 11:42:54 CET 2012
Advice on how to troubleshoot this would be appreciate.
Thank you.
Regards,
Isma
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