there additional flags are needed after editing?
Thank you,
Vincent Edwards
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ldn't have any actual impact on things as long as we returned to
version 7 to recon-all. I just want to confirm that my assumption is correct?
The pipeline would be: F7 (recon-all), F5 (edit with freeview), F7 (recon-all
for pial/wm/cp's)
Thanks,
ps%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg35901.html>
, but that was many years ago so I wanted to confirm.
Thanks,
Vincent Edwards
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that doesn't require switching Freesurfer versions?
Thanks for any help you can provide!
Vincent Edwards
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Please note that this e-mail is
: talsrcimg_to_3T18yoSchwartzReactN32_as_orig_t4pupuÀþN
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t4_read: transform initialized to I4
rotation matrix determinant 1.00
Thank you in advance! I appreciate any help!
Best,
Vinc
External Email - Use Caution
I have made manual edits to a subject that was initially run with the -FLAIR
and -FLAIRpial input flags. When I want to rerun freesurfer to
implement these edits should I add these flags again, or is it sufficient to
run recon-all -all?
External Email - Use Caution
Good morning Freesurfer Team!
I would like to use GLM on my longitudinal study to measure change between two
time points. I followed the longitudinal tutorial, and to my understanding, I
would move on to the general glm tutorial next. The longitudina
External Email - Use Caution
Thank you for your quick and positive reply.
Best,
Vincent
From: on behalf of Ruopeng Wang
Reply-To: Freesurfer support list
Date: Wednesday, 25 March 2020 at 16:41
To: Freesurfer support list
Subject: Re: [Freesurfer] Freeview CLI feature
set opacity for volumes, surface
overlays, and labels, but not for the surface itself.
2) Set smoothing iterations for isosurfaces
This can only be done in the GUI, not yet via the CLI.
Thank you for your consideration.
- Vincent
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ed in the expected number of users. Is
that an acceptable alternative to asking individual to obtain licenses?
Also, we can provide detailed usage statistics if there is interest.
Thanks,
Jim
--
James Vincent, PhD
BioGrids / SBGrid, Harvard Medical School
vinc...@hkl.hms.harvar
like to confirm this. Unfortunately, I did not receive any
reply to my emails to supp...@trackvis.org. Perhaps someone on this
list knows?
Thanks in advance!
Vincent.
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https://www.dropbox.com/s/ycav96v91e4ncbg/Cortex.png?dl=0
<https://www.dropbox.com/s/ycav96v91e4ncbg/Cortex.png?dl=0>
Thanks!
- Vincent
On Mon, 03 Jul 2017, Bruce Fischl wrote:
Hi Vincent
the putamen error probably means that the aseg is wrong, and if so, you can
correct the as
row of this image:
https://www.dropbox.com/s/x1euf9otl2nv6ff/Fix.png?dl=0).
I can’t find solutions for these particular issues under
https://surfer.nmr.mgh.harvard.edu/fswiki/Edits
How should I approach this? Suggestions are very much welcome.
Thank you!
- Vincent
Dear Anastasia,
I emailed with Dr. Knut Jørgen Bjuland because he had a similar issue
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg39745.html).
He mentioned that obtaining a new license could solve the issue. It did,
so my problem is resolved.
Best,
Vincent
TRACULA pushes multiple files as arguments to 'mri_convert
--frame', which is why I need the updated version.
Do you have any suggestions for me?
Thank you!
best,
Vincent
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Hi Vincent - Looks like an mri_convert error, so not specific to TRACUL
!
- Vincent
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to
eesurfer/dev>”.
I am particularly interested in a Linux version.
Would it be possible to open up access to the beta versions of Freeview to us
endusers again?
Thanks!
- Vincent
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includes full staff benefits, including
health insurance, and vacation time.
Interested candidates should send a cover letter and copy of their CV to Gino
Jackson, Administrative Officer, at gino.jack...@va.gov .
Vincent Corbo, Ph.D.
Postdoctoral fellow
Translational
must be a difference between FS 5.3 centos4, dev centos4 and dev
centos6 but I have no clue of what that could be or if it even matters.
I thought you might like to know.
Best,
Vincent.
On 17.05.2016 19:27, Martin Reuter wrote:
> Hi Vincent,
>
> I tried it on my machine and it
/recon_final/f5249_GD/tmp/BS_T1based//BS-DE-binaryMask_autoCropped.mgz
-lta trash.lta --mapmovhdr imageDump_coregistered.mgz --sat 50
Best,
Vincent
On 13.05.2016 16:13, Martin Reuter wrote:
> Hi Eugenio and Vincent,
>
> I cannot remember when I say robust_register crash the last
A funded postdoctoral position is available immediately (with start date in
summer 2016) to work in Dr. Rachael Seidler’s laboratory at the University of
Michigan studying brain and behavioral plasticity occurring with spaceflight
and analog environments. As one of the world’s leading research
Hello Freesurfer experts,
I would like to display stats images that are in MNI space on an MNI surface
volume.
I found this thread on the mailing list that explains how to use mri_vol2surf
to convert volumetric images to a surface:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-Ap
Hi everyone,
In the lh labels of fsaverage (FS 5.3 stable), vertices 102162 and
102163 seem to be incorrectly labeled in lh.cortex.label rather than
lh.Medial_wall.label. Anyone noticed this before? I didn't check rh yet.
Regards,
Vi
Cheap solution, use backticks to evaluate the string, e.g.
--reg /`echo $f1`/fsreg.dat
On 30.10.2014 15:33, Righart, Ruthger wrote:
> Dear Freesurfers,
>
> Not sure if my question is at the right place here but I'll give it a
> try.
> I have a memory disk with white spaces in the name: Se
segmented so differently.
On 26.08.2014 23:41, Douglas N
Greve wrote:
> And is that area outside of the brain not present in
the wm.mgz or
> filled.mgz on the good output? The orig.nofix should
hug the boundary of
> the wm.mgz
> doug
>
> On 08/26/2014 04:53 PM,
Vinc
in the other. Unfortunately this
type of error appears to be systematic in some of our data.
Vincent.
On 26.08.2014 16:22, Sebastian Moeller wrote:
> Hi Vincent hi
Melanie,
> please show us the *.orig surfaces on the critical slice. I
predict that these will be identical, If so you can
Dear all,
I was wondering if there is a way to use the segmentation of freesurfer
on a T2 weighted image only (without a T1 weighted image).
Sincerely
Vincent Noblet
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https
re maybe not correct
because after all the MAP is a part of all sampled paths.
Best, Vincent
Am 4/4/2014 11:49 AM, schrieb Anastasia Yendiki:
> Hi Vincent - I suspect that this problem would be fixed by some recent
> changes that I've implemented for the longitudinal stream of tracula, a
Dear TRACULA experts,
I have used the longitudinal version and find that for some subjects'
tracts Len_Min is larger than Len_Center. How is this possible? (An
extreme example is Len_Min: 36, Len_Max: 75, Len_Center: 4.)
Best, Vincent
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This email is free from viruses and malware be
analysis of the data in all_F*_skeletonised?
Best, Vincent
Am 10/11/2013 2:13 PM, schrieb Anastasia Yendiki:
>
> Hi Vincent - I'll take on the tracula-related parts:
>
> 2. For tracula, the part of the recon-all output that matters is the
> aparc+aseg. The surfaces will play a
t comprises the same number of voxels? This only differs BETWEEN
subjects as is pointed out later by your new feature?
Best,
Vincent
Am 12/9/2013 9:23 AM, schrieb Anastasia Yendiki:
> Hi all - I have just posted a tracula software update. This update adds
> some new functionality without a
f two subjects to get also 15 volumes
for the control group leaving 15 control and 21 experimental subjects
for the analysis (or for the next quality check that you proposed with
aparc+aseg..).
Thank you, again!
Best, Vincent
Am 10/17/2013 10:57 PM, schrieb Anastasia Yendiki:
>
>
.
How can I solve this problem?
Thanks,
Vincent
LOG FILE:
Tue May 7 13:58:41 EDT 2013
/Volumes/Data/tmp/Bedrest/FreeSurfer/8936
/Applications/freesurfer/bin/recon-all
-base 8936 -tp 8936_01 -tp 8936_02 -tp 8936_03 -tp 8936_04 -tp 8936_05 -tp
8936_06 -tp 8936_07 -all
subjid 8936
setenv
age to probabilities 0-1?
I don't believe dividing by 40 is correct, because that would mean that the
very few voxels will have a probability of being grey matter higher than 50%
(see the histogram).
Thanks in advance,
Vincent
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one smooth
shape. However, when I convert aseg or aparc structures to volumes, I don't
have this problem. Is it possible to get a a smooth, fully filled shape from a
Brodmann label?
Thanks in advance,
Vincent
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brainmask.gcuts.mgz
but using ls recursively and grepping for it, but I can't find it anywhere.
What explanations might there be for this? Thank you in advance.
::vincent
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Hi group,
I recently reconstructed a high-resolution 3D T1-weighted structural MRI using
Freesurfer. The subject had non-metallic extensions that were tied to her head
through a series of braids. Looking at the MRI in TkMedit, I can noticeably see
pieces of the extensions above her scalp. My gr
g dura/skull is
acceptable and how much cerebellum can be missing without affecting the
rest of the data. I've uploaded the file (AL.zip) to the FTP server. If
anybody has the time I would greatly appreciate it if I could have it
looked at. Thank you v
atures while stripping the skull, is not
used during this step. Why wouldn't you want to use it?
-- Vincent
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The information in thi
Hi,
I've uploaded my subject to the FTP server. The file is called AL.zip. I'm
really enjoying using freesurfer and I'm excited to hear what you think
about this subject. Thanks so much for the help.
-- Vincent
On Thursday, March 22, 2012 at 8:25 AM, Louis Nicholas Vinke wro
skull
and gcut not only fails to remove the skull but it removes cerebellum as
well. There is so much skull left that I am hesitant to try manual edits,
but I don't know any other options. Are there any? By the way, this brain
is from an older individual with pretty substantial atrop
recon-all
processing stream?
--Vincent
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The information in this e-mail is intended only for the person to whom it is
addressed. If you
Hi,
I'm trying to normalize ADC maps into a template image of my choice
using SPM8. In this purpose, I converted my DICOM files into nifti files
using "mri_convert" and now I would like to modify the origin of the
volumes.
Is that possible?
T
t; cd $FREESURFER_HOME/bin
> ldd ./mri_convert
>
> The rh9 build should work on the x86_64 architecture, but of course you
> can try the x86_64 build of freesurfer.
>
> Nick
>
> On Sun, 2007-02-18 at 14:04 -0500, Vincent Costa wrote:
> > Hi,
> >
> > I am at
Hi,
I am attempting to install Freesurfer on a system running Ubuntu 6.10
with x86_64 architecture.
On the Freesurfer Wiki it states that Debian users should install the
Red Hat 9 package. I went ahead and did this, setting up and
configuring Freesurfer following the directions listed on the Wik
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