Hi Bruce, i tried your suggestion but it is saying Missing file name. Do i need to include wm.mgz in the command line?


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 -s Subj2
if: Missing file name.
bash-4.1$

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Sent: 20 June 2017 19:10:10
To: Freesurfer support list
Subject: Re: [Freesurfer] Regenerating the WM Volume surface
 
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
>
>
>
>
>
>