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