can you include your full command line? It looks like you typed:
recon-all -autorecon2-wm -autorecon3 -Subj2
when probably what you wanted was
recon-all -autorecon2-wm -autorecon3 -s Subj2
cheers
Bruce
On Tue, 20
Jun 2017, Michael Davies wrote:
Hello, i am currently having problems with the code required to regenerate the
surface when editing the WM Volume. I was wondering if you could provide any
tips or advice as
to where i am going wrong please?
Kind regards, Michael
bash-4.1$ freesurfer_setup_freeview
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer_v6.0.0
FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects
MNI_DIR /usr/local/freesurfer_v6.0.0/mni
FSL_DIR /usr/local/fsl
bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj2/Subj2
bash-4.1$ recon-all -autorecon2-wm -autorecon3 -Subj2
ERROR: Flag -Subj2 unrecognized.
-autorecon2-wm -autorecon3 -Subj2
Linux pbic.bham.ac.uk 2.6.32-696.1.1.el6.x86_64 #1 SMP Tue Apr 11 17:13:24 UTC
2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s exited with ERRORS at Tue Jun 20 19:58:38 BST 2017
For more details, see the log file
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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