1. No, this is not a problem. The inflated.nofix is before the topology
correction and will have
2. 10 hours is reasonable depending on your harward environment.
3. Visual inspection is best
cheers
Bruce
defects. On Tue, 9 Jun 2015, Hassan bakhshi wrote:
> Hi All,
> I have 3 questions:
>
> 1
fig2 I guess, but if that fails you should probably give us more details
and Doug may be able to help you
cheers
Bruce
On Tue, 9 Jun 2015, lucas hosse wrote:
Dear Bruce,
I have these two types of functional volumes (in fig1 and fig2). Which one
do you suggest to use?
Thank again.
-
Lucas, also remember to include all previous correspondence. I've
already deleted the ones that had your command lines ...
doug
On 6/9/15 8:45 AM, Bruce Fischl wrote:
fig2 I guess, but if that fails you should probably give us more
details and Doug may be able to help you
cheers
Bruce
On Tue,
Hi Doug,
I think I've realized what the problem is - my cespct file has only one
frame
How can I run mkanalysis-sess, mkcontrast-sess and selxavg3-sess in a way
that produces the whole percent signal change time course?
Thanks
Jonathan
___
Freesurfer mail
Dear FS,
I received my license e-mail for the upteenth time and converted the
mail to license.txt in the $FREESURFER_HOME directory, but I stll get
an error message:
mri_convert
/home/rik88/GIfMI/Freesurfer/subjects/NMRD001/mri/rawavg.mgz
/home/rik88/GIfMI/Freesurfer/subjects/NMRD001/mri
About visual inspection!!!
Which images should I check??? And how can I understand the defect in
images?
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-ma
the defects are corrected and will be eliminated in the ?h.inflated, so
don't worry about the ones you see in the inflated.nofix. In the end what
you care about is making sure that the ?h.white surface follows the
gray/white boundary and the ?h.pial surface follows the gray/csf boundary
cheers
Hello,
Please refrain from sending the contents of the license file in the open
to the freesurfer list.
Unfortunately this is a known issue for all Opensuse platforms versions
greater than 12.1 and there are two potential solutions. The first is to
copy /lib64/libcrypt-2.14.1.so from an Opensu
Hi Hassan,
You should probably start by working through the tutorials:
https://surfer.nmr.mgh.harvard.edu/fswiki/Tutorials
This one covers that specific topic.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview
hth
d
On Tue, Jun 9, 2015 at 12:32 PM, Hassan bakhshi
wrote:
Hi,
I am trying to map a label in the left hemisphere to the right hemisphere.
To do so, I have registered the subject's native surfaces to the fsaverage_sym
template using
surfreg -s $subj -t fsaverage_sym -lh
surfreg -s $subj -t fsaverage_sym -lh -xhemi
What would be the best way to map the
Hello Freesurfer team
I got a warning message when I checked tkregister2 after I did mni152.reg,
mri_matrix_multiply command.
I got warning messages and found that the axial image was suddenly showed up on
coronal window view on tkregister2.
The error messages as follow like this:
[gencess:008
Hi,
I'm getting a bad magic number error using mri_convert. I'm trying to convert a
.nii file to a .mgz file. I've searched all over and all I can find is that you
can use python in another program to delete this number, and it is related to
the file extension. I've tried using the .nifti1 exte
Hi Jennifer
can MRIcro read it? Usually that means it is corrupted
Bruce
On Tue, 9 Jun 2015, Kriegel, Jennifer Lynn Sarai
wrote:
Hi,
I’m getting a bad magic number error using mri_convert. I’m trying to
convert a .nii file to a .mgz file. I’ve searched all over and all I can
find is th
MRIcro opens it, and so does SPM 8.
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Tuesday, June 09, 2015 3:02 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] bad magic number
Hi
how was it created?
On 06/09/2015 04:03 PM, Kriegel, Jennifer Lynn Sarai wrote:
> MRIcro opens it, and so does SPM 8.
>
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Tuesday, June
mricro
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Tuesday, June 09, 2015 3:16 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] bad magic number
how was it created?
On 0
Hello,
We are running on
Mac OSX 10.6.8
X11 version 2.3.6
Reading the download page recommends Xquarts 2.7.5 for 10.7
How important is the X11 requirment?
At this point (80 subjects freesurfed), is it recommended to update X11?
I warned about not upgrading operating system between studies, c
If you can open tkmedit then you do not need XQuartz.
https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer
If it doesnt open then you will most likely need it. Also, the X11
upgrade does not apply to the general rule against updating OS and/or
freesurfer versions.
-Zeke
On 06/09/2015
Carl,
You can modify the other 'dev' recon-all that was working to include the
fix. Find this line:
if($UseNewTopoFix ) then
which will be just above the line where orig_corrected is copied.
Change it to this:
if($UseNewTopoFix && -e ../surf/$hemi.orig_corrected ) then
Nick
On Sun, 2015-06-
Hi all,
I’ve recently completed surface reconstruction of macaque brain using Sebastian
Moeller’s pipeline (http://freesurfer.net/fswiki/MonkeyData) and now I’d like
to analyse retinotopic data and display it on the surface. However, when I try
running selx3avg-sess, I get this error: “ERROR: c
Dear FreeSurfer experts,
Schwartz et al (Neuroimage 103, 2014, 192-201) have demonstrated that T1W
WM signal increases with increased body adiposity, probably due to altered
brain lipid composition. This would affect cortical thickness measurements
in one of two ways: overestimating, in algorithms
Hi Ricardo
we do individual subject-level estimation of levels. And it could be a
confound I guess, although we use intensity gradients to definite
boundaries not absolute intensity levels, so we might be less prone to this
problem. If it shifts the apparent boundary there isn't much we can do
Hello,
Is there any way to have a black background / white font foreground for the
user interface on Freeveiw?
I am working in a dark reading room with others at times and the white user
interface reflects on other screens.
I noticed a dark mode for the command console on the preferences but i
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