Remove the '/' in front of "surf".

On 06/15/2017 11:45 AM, Michael Davies wrote:

Hi Bruce, i'm getting closer to opening it now. But the final command /surf/lh.pial \ didnt work this time. Any further suggestions?

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/Subj1/fsaverage
bash-4.1$ freeview -f \
> /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \
> /surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 \
> /surf/lh.inflated:visible=0 \
> /surf/lh.white:visible=0 \
> /surf/lh.pial \
> --viewport 3d
MRISread(/surf/lh.pial): could not open file
No such file or directory
MRISread failed
No such file or directory
ould not open file
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: 15 June 2017 15:19:21
To: Freesurfer support list
Subject: Re: [Freesurfer] viewing 3D surfaces

you are not calling freeview in this command. Try putting freeview at the
start
On Thu, 15 Jun 2017, Michael Davies wrote:

>
> Hi Bruce, i am still getting error messages. is there anything else i could
> try doing?
>
> 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/Subj1/fsaverage
> bash-4.1$ /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \
> >/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflat
> ed_thickness:visible=0 \
> > /surf/lh.inflated:visible=0 \
> > /surf/lh.white:visible=0 \
> > /surf/lh.pial \
> > --viewport 3d
> bash: /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0: No such
> file or directory
> 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: 15 June 2017 14:11
> To: Freesurfer support list
> Subject: Re: [Freesurfer] viewing 3D surfaces
> Hi Michael
>
> you need to have FreeSurfer in your path or nothing will work. Have you
> sourced the FreeSurferEnv.sh file? Have you set FREESURFER_HOME in the
> environment?
>
> cheers
> Bruce
>
>
> On Thu, 15 Jun 2017, Michael Davies wrote:
>
> > Hello, i am having problems accessing the 3D surfaces of my data. Is there
> > any advice you could provide for me please?
> > bash-4.1$ freeview -f \
> >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=apa
> r
> > c.annot:name=pial_aparc:visible=0 \
> >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:overl
> a
> > y=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0
> \
> >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:visib
> l
> > e=0 \
> >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.white:visible=
> 0
> > \
> > > /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial \
> > > --viewport 3d
> > bash: freeview: command not found
> >
> > Kind regards, Michael
> >
> >
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