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
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
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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Michael Davies