Hi Francesco,
You're not going to be able to run any of the dev-released binaries on a
centos4 VM. That's quite an old version. The minimum centos version that we
support now is v6. I think your best bet is download a centos 6 (or 7) VM and
install freesurfer 5 on that along with the dev freeview update. Rob, cc'd,
might have a FS 6.0 VM built somewhere, but even then you'll still need to
update freeview.
best,
Andrew
________________________________________
From: Francesco Puccettone <francesco.puccett...@gmail.com>
Sent: Tuesday, February 4, 2020 11:51 AM
To: Hoopes, Andrew; Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Highlighting single atlas structures in freeview
External Email - Use Caution
Hello Andrew-or others who might wish to help :-]
I've had to come back to this task after a while. I no longer have access to
the Linux PC, thus will need to do this on my Windows 10 installation of FS
(Oracle VM). What is the easiest way of achieving the task I described
(highlight a few brain regions in the DKT atlas)?
I tried updating FreeView as in the
updated<https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview> instructions,
but I am getting some no-space errors that I'd need to fix; also, this update
is in fact probably meant for direct Linux (not Windows VM) installations
anyway.
I see there is now a non-VM
way<https://surfer.nmr.mgh.harvard.edu/fswiki/WindowsSupport> of running FS on
Windows. However, since figures in older papers (such as Fig 1 in
this<https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0038511>
one) exist that show certain ROIs on a blank fsaverage, I still wonder whether
there is a way to do it with the standard VM image. The problem is, typing
freeview at my command line there still returns "bash:
/usr/local/freesurfer/bin/freeview: cannot execute binary file".
Thank you again for your help!
--Francesco
On Wed, 23 Jan 2019 at 15:38, Francesco Puccettone
<francesco.puccett...@gmail.com<mailto:francesco.puccett...@gmail.com>> wrote:
PS: I guess this is possible in older versions as well based on figures in
older papers (such as Fig 1 in
this<https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0038511>
one), that show certain ROIs on a blank fsaverage, just as I aim to do now.
--F.
On Wed, 23 Jan 2019 at 10:06, Francesco Puccettone
<francesco.puccett...@gmail.com<mailto:francesco.puccett...@gmail.com>> wrote:
Hi Andrew,
Thank you very much for this, I will give this a try when I next have access to
that PC, which will unfortunately not be very soon.
Until then, since the task I set out to do is quite straighforward, I was
wondering if there is a workaround to make the old Freeview (v5.3, which I
still consider an excellent and versatile tool) to do it as well, that is, to
highlight atlas parcels one at a time.
In either case I will report back once I am able to update those libraries.
Best,
--F.
On Tue, 22 Jan 2019 at 17:16, Hoopes, Andrew
<ahoo...@mgh.harvard.edu<mailto:ahoo...@mgh.harvard.edu>> wrote:
Hi Francesco, the linux dev distributions are built on 64bit centos6 and 7, so
you’re right about your original issue being related to the 32bit vm. I think
your newer Qt errors are related to out-of-date libraries supplied in the
‘Update Freeview’ instructions. I’ve just updated that wiki page (at
https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview) so it can account for
changing Qt libraries. Can you give those new instructions a try and let me
know how it goes?
thanks,
Andrew
From:
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Francesco Puccettone
<francesco.puccett...@gmail.com<mailto:francesco.puccett...@gmail.com>>
Reply-To: FS Help
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, January 22, 2019 at 5:40 AM
To: FS Help
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Highlighting single atlas structures in freeview
External Email - Use Caution
As per an older
thread<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2016-November/048719.html>,
this might be in fact due to the VM being 32bit. It is mentioned there the
64bit VirtualBox image is widely available, but I on the main FS website I can
only find the 32bit 5.3
version<https://surfer.nmr.mgh.harvard.edu/fswiki/Installation/FreeSurferVirtualImage>
for VirtualBox.
I also have a FS 6.0 64bit installation on a Linux PC, and I tried the same
update commands there. But there is still an error at the end when I try to
start freeview:
freeview: relocation error: freeview: symbol
_ZN17QAbstractItemView11eventFilterEP7QObjectP6QEvent, version Qt_5 not defined
in file libQt5Widgets.so.5 with link time reference
Thanks still..
--Francesco
On Tue, 22 Jan 2019 at 11:20, Francesco Puccettone
<francesco.puccett...@gmail.com<mailto:francesco.puccett...@gmail.com>> wrote:
Hi Ruopeng,
Thanks! I took those steps to update Freeview, but when I try to start (the
updated) Freeview, the command line returns "bash:
/usr/local/freesurfer/bin/freeview: cannot execute binary file".
Maybe there is something wrong in the update instructions, possibly the
library-update command (which has the -C option) or the chmod command?
I am using freesurfer-Linux-centos4-stable-pub-v5.3.0 inside an Oracle VM
Virtualbox.
--F.
On Mon, 21 Jan 2019 at 19:30, Ruopeng Wang
<rpw...@nmr.mgh.harvard.edu<mailto:rpw...@nmr.mgh.harvard.edu>> wrote:
HI Francesco,
The latest development version of freeview can do this. You can download it
from here:
https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview
Best,
Ruopeng
On Jan 21, 2019, at 8:54 AM, Francesco Puccettone
<francesco.puccett...@gmail.com<mailto:francesco.puccett...@gmail.com>> wrote:
External Email - Use Caution
Dear all,
I would like to show several structures from the DKT (or the Desikan-Killiany)
atlas alone on a "blank" fsaverage brain, rather than have all structures
displayed in different colors (as happens by default). For instance, I'd like
to just show "medialorbitofrontal" on its own, then "middletemporal" on its
own, etc.
After I open the parcellation,
freeview -v /FS/fsaverage/mri/aparc+aseg.mgz:colormap=lut:opacity=0.4 -f
/FS/fsaverage/surf/lh.white:annot=aparc.annot
, I expected to be able to turn each label in the list on and off like a layer,
but this does not work.
<21-01-2019 14.48.54.jpg>
I hoped I could use Alt+F to hide/show each atlas label at a time (cf freeview
tutorial<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview>),
but this instead toggles the entire external surface of the brain on and off.
Can anyone help? Thank you!
--Francesco
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