Message: 6
Date: Fri, 23 Sep 2016 18:53:45 -0400
From: Ruopeng Wang <rpwang@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] freeview display problem
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <732E27D8-179E-4B66-8762-7BF26C1DFF81@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Is there any error message on the terminal? What happens if you run ?glxgears? command? Does it run?
Best,
Ruopeng
> On Sep 23, 2016, at 4:35 PM, KALEY E ELLIS <keedwards2@wisc.edu> wrote:
>
> Hello FreeSurfer Developers,
>
> I am attempting to open freeview to view the brainmask on a subject in our study. Everything looks normal, except there is no image displayed (see attachment). Could you please let me know how I can fix this?
>
> Thank you,
> Kaley
>
> Associate Research Specialist
> Center for Healthy Minds
> Waisman Center for Brain Imaging and Behavior
> University of Wisconsin-Madison
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Message: 7
Date: Sat, 24 Sep 2016 11:36:46 -0400
From: Satrajit Ghosh <satra@mit.edu>
Subject: [Freesurfer] avoiding FSL when using T2pial
To: Freesurfer Mailing List <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CA+A4wOmXC6MVVyGLVsWtHotESOcR282mZba-U7Jy803KoOLURg@mail.gmail.com>
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hi doug,
without hacking recon-all is there a way to avoid using FSL when using the
T2pial flag?
cheers,
satra
#@# Refine Pial Surfs w/ T2/FLAIR Sat Sep 24 08:42:34 UTC 2016
bbregister --s sub-01 --mov /subjects/sub-01/mri/orig/T2raw.mgz --lta
/subjects/sub-01/mri/transforms/T2raw.lta --init-fsl --T2
Log file is /subjects/sub-01/mri/transforms/T2raw.dat.log
Sat Sep 24 08:42:35 UTC 2016
setenv SUBJECTS_DIR /subjects
cd /subjects/sub-01/scripts
/opt2/freesurfer/bin/bbregister --s sub-01 --mov
/subjects/sub-01/mri/orig/T2raw.mgz --lta
/subjects/sub-01/mri/transforms/T2raw.lta --init-fsl --T2
$Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
Linux b62492e050ac 4.4.20-moby #1 SMP Thu Sep 8 21:27:34 UTC 2016 x86_64
GNU/Linux
FREESURFER_HOME /opt2/freesurfer
mri_convert /subjects/sub-01/mri/orig/T2raw.mgz
/subjects/sub-01/mri/transforms/tmp.bbregister.4836/template.nii
mri_convert /subjects/sub-01/mri/orig/T2raw.mgz
/subjects/sub-01/mri/transforms/tmp.bbregister.4836/template.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /subjects/sub-01/mri/orig/T2raw.mgz...
TR=2500.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.0675638, -0.9838, -0.166052)
j_ras = (0.119725, -0.173224, 0.977578)
k_ras = (0.990505, -0.0461684, -0.129489)
writing to
/subjects/sub-01/mri/transforms/tmp.bbregister.4836/template.nii...
fslregister --s sub-01 --mov
/subjects/sub-01/mri/transforms/tmp.bbregister.4836/template.nii --reg
/subjects/sub-01/mri/transforms/tmp.bbregister.4836/reg.init.dat --niters 1
--maxangle 90 --nobetmov --tmp
/subjects/sub-01/mri/transforms/tmp.bbregister.4836/fslregister --dof 6
--fsvol brainmask.mgz
ERROR: you must have the FSLDIR environment variable defined and pointing
to the FSL installation
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