Try changing the thresholds (via the Configure button). When it first loads,
the thresholds are set very low. When they get changed to your values (4,5),
then there is nothing left and it looks like a blank brain.
On 7/6/2019 9:38 AM, Marie Hill wrote:
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Hi
Can you use mris_divide_parcellation
On 7/8/2019 1:27 PM, Mahshid Fouladivanda wrote:
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Dear Bruce,
All the outputs are .nii and .gii
I do not know if it is possible to convert it to the annotation!
By the way, what is needed for creation of the annotation
I think it is crashing outside of make_average_surface and make_average_volume,
so the log files are not telling me what is going on. Can you capture the full
terminal output? Also, you can try it with two subjects so that it runs faster
(but it might not crash).
On 7/10/2019 5:39 AM, Mads
It does not sound like something we can do, though I don't entirely follow
everything that you wrote
On 7/10/2019 11:07 PM, Maedeh Khalilian wrote:
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Dear FreeSurfer experts,
I know that FreeSurfer does segmentation, surface reconstruction and topology
On 7/15/2019 12:50 PM, Tugce Duran wrote:
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Hi Dr. Greve,
I am interested in designing the Face Name Associative Memory Exam (FNAME) fMRI
task for our study.
There are 80 face-name pairs that we will use and the duration can be between
3.5 and 4.75 secs. I
For question 1, try this
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
You did not say which MNI space you were dealing with (we use mni305, not 152).
On 7/15/2019 12:02 PM, Zhi Li wrote:
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Thank you very much, Tim. Any idea for the 1st
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I try again with fortran, uploaded it again, and now I get this message:
jcrn12@jcrn12-VirtualBox:~$ freeview
This application failed to start because it could not find or load the Qt
platform plugin "xcb"
in "".
Reinstalling the application may fix
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libgfortran.so.3. No found.
I día the fortran step as you indicated yo me.
Thanks again,
JC.
-- Mensaje reenviado -
De: fsbuild
Fecha: El lun, 15 de jul. de 2019 a las 17:09
Asunto: Re: [Freesurfer] freeview
Para:
Cc:
Did you try,
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Did you try,
$ ldd /usr/local/freesurfer/bin/freeview | grep not
?
- R.
On Jul 12, 2019, at 08:42, Juan Rivas jcr...@gmail.com
wrote:External Email - Use
CautionIt looks like freeview
is in: jcrn12@jcrn12-VirtualBox:~$
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It looks like freeview is in: jcrn12@jcrn12-VirtualBox:~$
/usr/local/freesurfer/bin/freeview
But when I try to use it, I can not do it, because: jcrn12@jcrn12-VirtualBox:~$
ldd freeview | grep not
ldd: ./freeview: No such file or directory.
Thank you
you need to run:
ldd /usr/local/freesurfer/bin/freeview | grep not
cheers
Bruce
On Fri, 12 Jul 2019, Juan
Rivas wrote:
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It does not work:jcrn12@jcrn12-VirtualBox:/usr/local/bin$ which freeview
/usr/local/freesurfer/bin/freeview
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It does not work:
jcrn12@jcrn12-VirtualBox:/usr/local/bin$ which freeview
/usr/local/freesurfer/bin/freeview
jcrn12@jcrn12-VirtualBox:/usr/local/bin$ ldd freeview | grep not
ldd: ./freeview: No such file or directory
JC
-- Forwarded message
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Sorry - from your previous mail, I mistakenly thought “which freeview” returned
/usr/local/bin/freeview.
If you can reproduce what you did before to run freeview from the command line
where it tells you that it was not finding libgfortran, then
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That is what happened:
$ ldd /usr/local/bin/freeview | grep not
ldd: /usr/local/bin/freeview: No such file or directory
$ bash
jcrn12@jcrn12-VirtualBox:~$ ldd /usr/local/bin/freeview | grep not
ldd: /usr/local/bin/freeview: No such file or directory
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That is what happened:
$ ldd /usr/local/bin/freeview | grep not
ldd: /usr/local/bin/freeview: No such file or directory
$ bash
jcrn12@jcrn12-VirtualBox:~$ ldd /usr/local/bin/freeview | grep not
ldd: /usr/local/bin/freeview: No such file or directory
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Hi Dr. Greve,
I am interested in designing the Face Name Associative Memory Exam (FNAME) fMRI
task for our study.
There are 80 face-name pairs that we will use and the duration can be between
3.5 and 4.75 secs. I have used the following command:
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Hello JC,
Try this to see what libs are missing,
$ ldd /usr/local/bin/freeview | grep not
- R.
On Jul 12, 2019, at 06:19, Juan Rivas jcr...@gmail.com
wrote:External Email - Use
CautionHi, thank you for your
help.I tried again and once again it did
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Hello Robin,
I believe folks use the freesurfer binary archive expanded/installed on file
servers that are remotely mounted, e.g., thru NFS, so everyone can share a
common installation. IT/dev-ops can implement that in different ways,
e.g., maybe
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Hi, thank you for your help.
I tried again and once again it did not work. I am using Ubuntu 18
This is the message I get:
$ freeview
sh: 8: freeview: not found
$ which freeview
$ /usr/local/bin/freeview
sh: 10: /usr/local/bin/freeview: not found
$
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-- Forwarded message -
De: Juan Rivas
Date: vie., 12 jul. 2019 a las 3:02
Subject: Re: [Freesurfer] Freeview
To: fsbuild
Hi, thank you for your answer.
I did what you recommended to me, and I get this message:
freeview: error while
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Thank you very much, Tim. Any idea for the 1st question?
Thanks and best wishes,
Lizhi
On Sat, 13 Jul 2019 at 09:18, Tim Schäfer wrote:
> External Email - Use Caution
>
> Dear Lizhi,
>
> on your 2nd question: a rough explanation is on the
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Hello JC,
Your machine could be missing the qt5 libraries/files.
On Ubuntu linux you can try installing them with,$sudo apt-get install
qt5-default qtcreatorlibqt5x11extras5-dev
On CentOS linux,$sudo yum install qt-create qt-config.x86_64$sudo
yum
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Hello, I am trying to use freeview, but everytime I try I get this message:
freeview: error while loading shared libraries: libQt5Widgets.so.5: cannot
open shared object file: No such file or directory.
How can I fix it?
Thanks a lot,
JC.
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Hello,
The Center for Cognitive and Behavioral Brain Imaging (CCBBI) at The Ohio
State University is seeking to hire a Magnetic Resonance Imaging (MRI)
Technologist. Please see attached document for full description.
Best Regards,
The Clinical
The ribbon.mgz file should be about the same (but for both hemis)
On 7/15/2019 9:36 AM, Bruce Fischl wrote:
Hi Marina
if you have a pial surface you can use mris_fill to fill the interior then use
that as a mask
cheers
Bruce
On Mon, 15 Jul 2019, Marina Fernández wrote:
External
that or see here
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On 7/15/2019 9:39 AM, Bruce Fischl wrote:
you can do this with mri_convert:
mri_convert -rl native_volume.mgz -rt nearest apas+head.mgz apas+head.native.mgz
cheers
Bruce
On Mon, 15 Jul 2019, Laboratorio de
you can do this with mri_convert:
mri_convert -rl native_volume.mgz -rt nearest apas+head.mgz apas+head.native.mgz
cheers
Bruce
On Mon, 15 Jul
2019, Laboratorio de
Neurociencia Funcional wrote:
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Thank you, Doug. The voxel resolution of the
Hi Marina
if you have a pial surface you can use mris_fill to fill the interior then
use that as a mask
cheers
Bruce
On Mon, 15 Jul 2019, Marina Fernández wrote:
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Dear experts,
I need to get a no-skull brain. The automated no-skull brain has
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Thank you, Doug. The voxel resolution of the apas+head.mgz file is 1mm3.
Would it be possible to obtain the same file but with the native resolution?
Best,
Jose
El lun., 15 jul. 2019 a las 6:01, Greve, Douglas N.,Ph.D. (<
dgr...@mgh.harvard.edu>)
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Hi folks,
I am new to the Freesurfer world and I have a couple of questions about
installing the application, specifically around the 10Gb "footprint" of data,
after unpacking the archive file.
So I have run through the installation and
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Dear experts,
I need to get a no-skull brain. The automated no-skull brain has many
errors and I was thinking that I could create it taking into account the
gray matter mask (we segment manually, so the mask is accurate) in such a
way that everything
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