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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