no, we don't. Is that affecting the brain?
On 04/12/2018 05:26 PM, John Anderson wrote:
> Dear Freesurfer experts,
> I would like t inquire if there is any tool or method in Freesurfer
> that can help to fix susceptibility artifacts in T1 image like attached
>
>
> Any suggestion is highly apprec
yes,, there is a command line option (-ss I think)
cheers
Bruce
On Thu, 12 Apr 2018,
Douglas N. Greve wrote:
We are not really supporting tksurfer anymore. You can use freeview to
save a png from the GUI. Ruopeng, is there a way to take a snap shot
from the command line?
On 04/12/2018 10:29
Child Mind Institute is seeking a Data Analyst to join our team. The Data
Analyst’s role is to assist and support the acquisition, manipulation, and
analysis of data, as well as the reporting results. In particular, our work
includes: 1) support the preprocessing of large fMRI dataset in human and
Dear Kersten,
Thanks for reply. I have new question.
When I set model use total_i_vol_stats = lme_fit_FS(X,[1 2],Y(:,2),ni)
and total_i_vol_stats = lme_fit_FS(X,[1],Y(:,2),ni).
But Bhat of two models' year have a lot different, for example, with 2 is
1.2422 without 2 is -0.5737. The direction has
If you want to test for an interaction between Age and Weight, you need
to create a new covariate which is Age*Weight, then test the sig of this
covariate. I would demean Age and Weight for both the inidvidual
covaraite and before computing the product.
On 04/12/2018 12:35 PM, David S Lee wrot
Right. And you'd need to redo it after all manual edits
On 04/12/2018 11:06 AM, Alexopoulos, Dimitrios wrote:
>
> Thanks. We are starting an analysis of a pediatric cohort using FS 6.0
> and may/may not use QDEC downstream for surface-based group analysis.
>
> That said, it sounds like it is not
Ok, thanks for the reply. It sounds like the ENIGMA folks need to updage their
commands to use freeview. I'll try using ImageMajick's import as a workaround.
Jen
Message: 11
Date: Thu, 12 Apr 2018 10:59:58 -0400
From: "Douglas N. Greve"
Subject: Re: [Freesurfer] tksurkfer save erro
Thank you very much!!
De: freesurfer-boun...@nmr.mgh.harvard.edu
en nombre de Douglas N. Greve
Enviado: jueves, 12 de abril de 2018 16:39
Para: freesurfer@nmr.mgh.harvard.edu
Asunto: Re: [Freesurfer] RV: "preproc-sess" with intermediate volume
Hi David, move yo
Hi FreeSurfer Experts,
I have two groups (Male and Female) and two covariates (Age and Weight). I
want to test change of cortical thickness with age and weight, after
removing effects of Group. In other words, is there an interaction between
age and weight, regressing out the effects of groups.
H
Hi,
I was wondering if there was any existing freesurfer script to calculate
the roundness and/or the perimeter of a surface label? If anyone has ideas
on how to calculate this, I would appreciate it.
Thanks,
Jonathan
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Hello Bennet,
Maybe someone else can chime in on this, as I have not worked on a system
with FIPS, but perhaps there is a way for the FIPS administrator to white list
all the Freesurfer binaries (and the license file), as security exempt.
I know some Enterprise/business applications like Adobe’s
Thanks. We are starting an analysis of a pediatric cohort using FS 6.0 and
may/may not use QDEC downstream for surface-based group analysis.
That said, it sounds like it is not a bad idea use -qcache other than more
preprocessing time.
Basically, same output as without -qcahe but more files creat
We are not really supporting tksurfer anymore. You can use freeview to
save a png from the GUI. Ruopeng, is there a way to take a snap shot
from the command line?
On 04/12/2018 10:29 AM, Evans, Jennifer (NIH/NIMH) [F] wrote:
>
> Hi,
>
> This is a repost as I didn’t get a reply to the one I sent
Hi Jen
tksurfer is deprecated and this sounds like an error in your graphics
environment. Have you tried using freeview instead? Generating snapshots
should be pretty easy
cheers
Bruce
On Thu, 12 Apr 2018, Evans, Jennifer (NIH/NIMH) [F]
wrote:
Hi,
This is a repost as I didn’t g
Matlab is not needed for basic FS analysis. I think the only things it
is used for in FS is hippocampal subfields, FSFAST, and lGI. I don't
think there are any limitations, but I'm not sure. I don't know about spm12
On 04/10/2018 01:35 PM, John Absher wrote:
>
> Hi,
>
> I was pleased to learn f
It appears that FreeSurfer is not compatible with systems for which
FIPS level security is mandated. In our case, I am told this is part
of our data use agreement with the VA.
We tried to run it, and I get the following stack trace showing what
appears to be license validation using the crypt() f
Hi Srishti, you will need to be much more specific to allow me to help
you. mni152_subject is not a file that can be input to recon-all (it
should be a dicom or nifti or mgz). If you use the same input to
recon-all that you used to view it in spm, then the FS output should
align with your map.
Hi David, move your intermediate volume to
session_1/ifsd/001/orig.mgz
then try
-bbr-int ifsd orig
On 04/12/2018 04:10 AM, David Sánchez Bestué wrote:
> Dear all,
>
> I have a problem with the command:
> "preproc-sess"
>
> I wanted to use the Registration option to add an intermediate volume
Hi,
This is a repost as I didn’t get a reply to the one I sent a few weeks ago.
This error basically means I can’t automatically generate a webpage of all of
the segmentation results. I getting an error when trying to save a tiff file
using tksurfer on a linux machine via NoMachine v5.0.47.
What is the "MNI template" that you are using. I mean an exact file
used. Did you use this file when you ran recon-all?
On 04/12/2018 10:23 AM, srishti goel wrote:
> Yeah, I am unsure where to go from here as well. So the results can be
> viewed in SPM and on the MNI template space itself, sinc
Yeah, I am unsure where to go from here as well. So the results can be
viewed in SPM and on the MNI template space itself, since SPM typically
does not have a problem showing multiple images in different sizes.
Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Exper
When you use bbregister, it is expecting the input nii file to represent
the actual anatomy of the subject, so it does not surprise me that it
does not work that well. I'm not sure what to do about this because a
meta analysis image will never have decent anatomy. In theory, it should
be alread
We would like to inform you that the abstract submission deadline to
PREDICTIVE PROCESSING has been extended. The new deadline is April 16th.
The conference dates are June 20-22, 2018
Dear Researcher,
We are happy to announce the new discussion arena fully centred on
predictive processing. The W
Hi all,
Would you recommend using the 3t flag for recon-all when analyzing data from a
3t scanner? I read about it in some papers but not everybody seems to use it.
Also, do you know whether the flag can be used in the longitudinal stream as
well or does it only apply to the crosssectional proc
Thanks for all the help and explanation, Anastasia.
Best - Don
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 9:18 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-a
Apologize for multiple posting ***Dear Colleagues,We are delighted to
invite you to join us for the MLCN 2018 workshop as a satellite event of
MICCAI 2018 conference, Granada, Spain.
---
*Postdoctoral position in the Team “Multimodal Neuroimaging and Lifestyle
in Aging and Alzheimer’s disease” (Dr. Gaël Chételat , UMR-S U1237-PhIND,
Caen, France) ** Duration: 2 years (1 year renewable 1 year).
* Starting date: June 2018
* Research team: Multimodal Neuroimaging and Lifestyle in Agin
Dear all,
I have a problem with the command:
"preproc-sess"
I wanted to use the Registration option to add an intermediate volume. The only
documentation I could find about it was the one that appears with the command:
"preproc-sess --help"
Registration options
-init-fsl : use fsl to initia
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