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Dear FreeSurfer experts
I ran QDEC and got the following error.
Design matrix --
1.0 1.04000 -1.38574 2.0 29.0 19.0;
1.0 1.04000 -0.55066 2.0 35.0 19.0;
1.0 1.03000 2.31721
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Hello FS team,
can you please tell me what is the measurement scale of the curv.mg file?
Is it a mean curvature (mm-1) or a gaussian curvature (mm-2)? I got values
between 0.02 and -0.08 and it seems they are gaussian curvature.
Thanks a lot for your
sorry, for the delay. The par files are both empty and that link cannot be
found (maybe expired)
On 1/15/2020 11:24 AM, Marco Ninghetto wrote:
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Sorry for the late reply, the message was non stop bounced.
So, here You will find:
- terminal output for `selxavg
Actually, I was able to get those files from your previous emails
On 1/15/2020 11:24 AM, Marco Ninghetto wrote:
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Sorry for the late reply, the message was non stop bounced.
So, here You will find:
- terminal output for `selxavg3-sess` (filename: terminal_outp
You can try freeview, but there might be something wrong with the label. How
was it created?
On 1/16/2020 11:51 PM, Tien Pham wrote:
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Thank you for your help.
I cannot load the label on surface, this is the error:
[toyama-no-iMac:/applications/freesurfer/sub
For the mgz volumes, you should be able to do something like
mri_add_xform_to_header -c /new/path/to/xfm brain.mgz
For the labels you could just use something like
sed s/oldsubjectname/newsubjectname
On 1/17/2020 3:48 AM, Tim Schäfer wrote:
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>
> Hi Dougl
Hi Rafael
the ?h.curv files are spatially smoothed mean curvature
cheers
Bruce
On Tue, 21 Jan
2020, Raffaele Dubbioso wrote:
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Hello FS team,
can you please tell me what is the measurement scale of the curv.mg file?
Is it a mean curvature (mm-1)
Which version of FS are you using? I don't have this problem in v6 or dev. What
OS are you using?
On 1/17/2020 9:09 AM, Marcos Martins da Silva wrote:
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Thank you, Doug! Yes, there is an option to load a fsgd file in Freeview, but
when you try to use this op
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Hi Doug,
thanks for the mri_add_xform_to_header idea, I didn't know about that option!
Best,
Tim
> On January 21, 2020 at 4:24 PM "Greve, Douglas N.,Ph.D."
> wrote:
>
>
>
> For the mgz volumes, you should be able to do something like
> mri_add_
On 1/17/2020 10:39 AM, Graduate Imaging wrote:
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Hello,
I recently ran a vertex wise analysis on two different projects the first had
three groups with three co-variates that looked at if group membership was
associated with brain volume. The second project
Don't smooth them! Smoothing creates partial volume effects. When you convert
to nifti, you have to be careful to make sure that any DICOM intensity scaling
is taken into effect; it is becoming more common these days. The only other
thing may be to remove the gradient distortion from the MRI if
Try normalizing your covariates (ie, remove the mean and divide by the stddev)
On 1/21/2020 7:39 AM, vittal korann wrote:
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Dear FreeSurfer experts
I ran QDEC and got the following error.
Design matrix --
1.0 1.04000 -1.38574 2.0
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Thank you for your reply. I think I've better explained the situation in a
further email, which I paste in here.
I used expanding ring and rotating wedge. For my pilot, unfortunately, we
used only 2 cycles for each stimulus and 1 cycle lasted 200 secon
Hello FreeSurfer Developers,
I'm attempting to run recon-all after unpacking data. It is exiting with errors
- mri_cc: no WM voxels found with norm > 40 -- check skull stripping
I've attached the recon-all.log in case it's of any use.
1) FreeSurfer version:
freesurfer-Linux-centos7_x86_64-
Hello FreeSurfer Developers,
I'm attempting to run recon-all after unpacking data. It is exiting with errors
- mri_cc: no WM voxels found with norm > 40 -- check skull stripping
I've attached the recon-all.log in case it's of any use.
1) FreeSurfer version:
freesurfer-Linux-centos7_x86_64-st
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FreeSurfer 6 over CentOS 7. I have the same problem with 5.3 too. One more
information: CentOS 7 is configured as PT-br instead of English. Could it
be the reason?
Em ter, 21 de jan de 2020 12:29, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> escre
Hi Alex,
If the there is volume geometry information in the surface header, freeview
will display the surface in that coordinate. Otherwise it will display it in
surfaceRAS. The center of the view is automatically set as the center of FOV of
the surface.
Best,
Ruopeng
> On Jan 19, 2020, at 7:
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Dear Freesurfer experts,
I try to run several subjects one after each other on recon-all using:
for SubjectName in `cat *subs2.txt*`; do recon-all -i
$SUBJECTS_DIR/$SubjectName/* -all -qcache; done
Output:
ERROR: Flag
/Users/benine/Desktop/PVS_validat
You can only specify one input dicom file. We have a tutorial on how to
find that one file in a subject. See
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Practice
On 1/21/20 3:58 PM, Benjamin Ineichen wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer experts,
>
> I try to
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Hi, Tim,
the subject ID can be also contained in the commandline history which is stored
in .mgz files. This can be viewed using
mri_info file.mgz --cmds
I am not aware of any direct command which can strip out this info, but you
surely could conver
Hi Antonin and Tim
you should be able to do:
setenv FS_SKIP_TAGS 1
mri_convert vol_with_tags.mgz vol_without_tags.mgz
and verify it worked with mri_info
cheers
Bruce
On Tue, 21 Jan 2020, Antonin Skoch wrote:
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Hi, Tim,
the subject ID can be also c
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Thank you, Doug.
Sorry for the misunderstanding but the folders for the individual subjects
in my SUBJECTS_DIR already contain only the T1-MPRAGE-DICOMS and I only
want to feed one DICOM per patient to the recon-all. My problem is the
batch processing
I've answered one of your questions below.
Ruopeng, there is a question for you too
On 1/21/20 11:02 AM, Assis Lopes, Pedro Augusto wrote:
> Hello Freesurfer experts!
>
> Thank you so much for the explanation Dr. Greve! Attached is the output of
> our overlaid surfaces:
>
> 1 - Grossly sp
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Thank you for your e-mail.
I also could not load the label in freeview. The terminal showed the
following error:
2020-01-22 09:56:18.064 Freeview[51338:303] modalSession has been exited
prematurely - check for a reentrant call to endModalSession:
2020
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Dear Douglas
I did normalize ICV values. This is something else I guess.
With regards
Vittal
On Tue, Jan 21, 2020 at 6:09 PM vittal korann
wrote:
> Dear FreeSurfer experts
>
> I ran QDEC and got the following error.
>
> Design matrix
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Dear FS experts,
I came across this post about a bug related to global measures of volume from
version 6.0:
https://surfer.nmr.mgh.harvard.edu/fswiki/BrainVolStatsFixed
I have two questions that I hope someone can clarify:
1) This bug does not affect
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