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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 <AHOOPES@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 I think your newer Qt errors are related to out-of-date libraries supplied in the ‘Update Freeview’ instructions.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-bounces@nmr.mgh.harvard.edu> on behalf of Francesco Puccettone <francesco.puccettone@gmail.com>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, January 22, 2019 at 5:40 AM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Highlighting single atlas structures in freeview

 

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As per an older thread, 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 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.puccettone@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 <rpwang@nmr.mgh.harvard.edu> wrote:

HI Francesco,

 

The latest development version of freeview can do this. You can download it from here:

 

 

Best,

Ruopeng



On Jan 21, 2019, at 8:54 AM, Francesco Puccettone <francesco.puccettone@gmail.com> wrote:

 

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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), but this instead toggles the entire external surface of the brain on and off.

 

Can anyone help? Thank you!

--Francesco

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