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=inflated_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=apar
> c.annot:name=pial_aparc:visible=0 \
> >/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:overla
> y=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 \
> >/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:visibl
> 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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