Dear Doug,
thank you so much for the feedback and all of your help!
Best wishes
Marco
On Thu, Jul 6, 2017 at 1:45 AM, Douglas Greve
wrote:
> You can use mri_surfcluster. Set the sig.mgh as the --in file. Set --fdr
> to the FDR you want. Set --subject fsaverage
Stanford University's Department of Psychiatry & Behavioral Sciences is seeking
to hire full time post-doctoral fellows in Computational Modeling of Brain
Networks for their Cognitive & Systems Neuroscience Laboratory.
This lab is headed by Dr. Vinod Menon who has broad multidisciplinary
Stanford University's Department of Psychiatry & Behavioral Sciences is seeking
to hire full time post-doctoral fellows in Computational Modeling of Brain
Networks for their Cognitive & Systems Neuroscience Laboratory.
This lab is headed by Dr. Vinod Menon who has broad multidisciplinary
Dear freesurfer developers,
I’d like to ask about an error I encountered in Freesurfer v6.0 with
mkbrainmask-sess. I am using macOS Sierra.
Here is the error:
error:"ERROR: cannot find
/Users/lguo15/Documents/MATLAB/fMRI_P3/Fisch_P3_01/bold/register.dof6.lta, you
might need to run
then you shouldn't be sourcing a script that uses setenv. Try sourcing
$FREESURFER_HOME/FreeSurferEnv.sh
cheers
Bruce
On Tue, 11 Jul 2017, Yagmur Ozdemir 19
wrote:
It is using bash.
Idil
From: freesurfer-boun...@nmr.mgh.harvard.edu
Thanks for your reply,
I have a follow up on my first question - if however I was not looking for
a main effect of gender, but for the main effect of something else (e.g.
diagnosis), will it then be ok to include the unbalanced group (i.e.
A-male), to control for gender?
Thanks!
Regards
Yann
Dear Bruce,
To be honest, I'm not sure, but I think I want the average of the scalar fields
over the surface. I want to have some way of putting the thickness overlays on
the surfaces of all my subjects together and visualizing this (I have pre-post
data so I'd like to have a visualization of
It is using bash.
Idil
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Tuesday, July 11, 2017 6:30 PM
To: Freesurfer support list
Subject: Re: [Freesurfer]
Hi Idil
do you know what shell you are using in the terminal that you are trying
to call freeview from?
On Tue, 11 Jul 2017, Yagmur Ozdemir 19 wrote:
Hello,
I only followed the steps in the install/download page and installed tcsh
because it was not running recon-all. Are you saying that I
Hello,
I only followed the steps in the install/download page and installed tcsh
because it was not running recon-all. Are you saying that I should set up
freeview by sourcing those three files and use the *.csh extension? When
opening the terminal again after recon-all to run this I did not
Hi Idil
how do you setup freesurfer? If you are using bash (and it looks like you
are) you should source the *.sh file, not the *.csh. Also, note that you
should use T1.mgz not T1/mgz in your freeview command line
cheers
Bruce
On Tue, 11 Jul
2017, Yagmur Ozdemir 19 wrote:
Hello,
I am
Hello,
I am installing Freesurfer with my limited coding knowledge and this problem
with freeview came up when I was trying to view the volumes of recon-ed subject.
lab@lab-ThinkStation-E31:~/Desktop/freesurfer/subjects$ freeview -v
practice/mri/T1/mgz
No command 'freeview' found, did you
sure. I'll leave the rest to Doug except to say that a full head EPI is a
pretty cheap and useful thing to get, and that it is not surprising the
using the header (assuming they are same session) works better than
anything else
cheers
Bruce
On Tue, 11 Jul 2017, Paul Glad Mihai wrote:
> Hi
Hi Glad
can you send us the full command line you are using and screen output?
thanks
Bruce
On
Tue, 11 Jul 2017, Paul Glad Mihai wrote:
> Dear List,
>
> I've been quite frustrated with the BBRegister results when trying to
> register a partial field of view EPI mean functional image to a T1
Dear List,
I've been quite frustrated with the BBRegister results when trying to
register a partial field of view EPI mean functional image to a T1 scan.
I've tried different init arguments (fsl, spm, header) and none really
work. I've found that the initial registration is causing the problem,
Dear Freesurfer Team,
I am attempting to complete a surface reconstruction on a dataset with
traumatic lesions both to the grey and white matter.
I am hoping to get some opinions on what would be considered as the 'Best
practice' pipeline for dealing with such a dataset. We have access to T1
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