Thank you for your help Bruce. I have downloaded Unix_tutorial_FS_course. Is there any others you could recommend?


Michael




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 17:03:19
To: Freesurfer support list
Subject: Re: [Freesurfer] viewing 3D surfaces
 
I mean the /surf/lh.pial path has to be wrong, as that points to the root
where you wouldn't be allowed to put data. I guess surf/ worked for you,
but would only work if you were in the $SUBJECTS_DIR/$subject dir when you
issued the freeview command.

cheers
Bruce


On Thu, 15 Jun 2017, Michael
Davies wrote:

>
> Hello Bruce, how do you mean the path is wrong? I am curious as the data
> loaded just.
>
>
> Kind regards, Michael
>
> ____________________________________________________________________________
> 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 16:11:53
> To: Freesurfer support list
> Subject: Re: [Freesurfer] viewing 3D surfaces  
> Hi Michael
>
> I think you need to do a Unix tutorial. That path is wrong.
>
> cheers
> Bruce
>
>
> On Thu, 15 Jun
> 2017, 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=infla
> t
> > ed_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=infl
> a
> > t
> > > 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=a
> p
> > a
> > > r
> > > > c.annot:name=pial_aparc:visible=0 \
> >>>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:ove
> r
> > l
> > > a
> > > >
> > y=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0
> > > \
> >>>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:vis
> i
> > b
> > > l
> > > > e=0 \
> >>>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.white:visibl
> e
> > =
> > > 0
> > > > \
> > > > > /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial \
> > > > > --viewport 3d
> > > > bash: freeview: command not found
> > > >
> > > > Kind regards, Michael
> > > >
> > > >
> > > _______________________________________________
> > > Freesurfer mailing list
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> > > mail.nmr.mgh.harvard.edu
> > > To see the collection of prior postings to the list, visit the
> Freesurfer
> > > Archives. A searchable archive which of messages PRIOR to March 2004 is
> at
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