as a numeric variable with
> values 0 and 1, rather than splitting up my other categories?
>
> Thank you for your help,
> -Eric
>
> On Thu, Aug 13, 2020 at 9:42 AM Douglas N. Greve
> wrote:
>
>> Do you have a 1-off error? Ie, FS starts counting at 0 and matla
,
-Eric
On Thu, Aug 13, 2020 at 9:42 AM Douglas N. Greve
wrote:
> Do you have a 1-off error? Ie, FS starts counting at 0 and matlab starts
> counting at 1. So vertex 53263 is vertex 53264 in matlab.
>
> On 8/12/2020 5:31 PM, Eric Cunningham wrote:
>
> External Email - U
External Email - Use Caution
Hello Freesurfer Experts,
I am trying to plot the ${meas} values at the maximum vertex in a
significant cluster found by the group analysis pipeline (mri_glmfit).
I created an .mgh file with mris_preproc, rh.cbd7.area.10.mgh. I read this
file into
External Email - Use Caution
Dear Freesurfer Experts,
I have recently processed some data with the following 2 steps:
1) Perform skullstripping outside freesurfer to generate a nifti file
(mostly using AFNI).
2) Run that through freesurfer using the -noskullstrip flag.
Comparing
Greetings Freesurfer experts,
The README file in the $SUBJECTS_DIR says that a different directory can be
specified by setting the env var SUBJECTS_DIR prior to the 'source
$FREESURFER_HOME/FreeSurferEnv.csh' statement.
Do the original contents of SUBJECTS_DIR (such as fsaverage) need to be
Other than fsaverage, are there any other files that need to be linked for
recon-all to work?
Thanks
On Mon, Nov 23, 2015 at 4:57 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
> Hi Eric
> No, you can just symlink fsaverage and such
> Cheers
> Bruce
>
> > On Nov
Hello Freesurfer Experts,
I am trying to reproduce the values in sig.mgh using matlab, just to
confirm that I know what is going on. My numbers do not match exactly, and
I am hoping someone can explain my error, or point me in the right
direction.
With Qdec, I built a model with one discrete
Hello Freesurfer Experts,
Our group is trying to determine the importance of manual edits on our
data. After discovering poor white matter segmentation in the
supramarginal/inferiorparietal regions, we performed manual edits as
described in the FsTutorial.
Surprisingly, the areas we edited had
is attached.
Please advise,
Thank you,
-Eric Cunningham
recon-all.log
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is attached.
Please advise,
Thank you,
-Eric Cunningham
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Hello Freesurfer experts,
I am getting some unusual results with the lme pipeline, and I would
appreciate help with identifying the most likely step in which the problem
may have originated.
Running lme_fit_FS.m on a single vertex, followed by lme_F on the output of
that (stats) yields a p-value
Hello Freesurfer experts,
The lme_mass_vw script runs for a long time and outputs info into the
matlab terminal. Most look like this:
Location #: Algorithm did not converge. Initial and final likelihoods:
###, ###
Running this script, for almost every line, the initial and final
Hello Freesurfer experts,
I have a question about how to determine if a covariate is important in a
mixed effects model
for example:
Y1 = B1 + B2(time) + B3(rand_effect1) + B4(rand_effect*time) +
B5(covariate_1) +B6(covariate_2)
Y2 = B1 + B2(time) + B3(rand_effect1) + B4(rand_effect*time) +
(covariate_1)
The difference between the two that I was trying to highlight is the
presence of the second covariate term.
Thanks,
-E
On Tue, Mar 4, 2014 at 11:18 AM, Eric Cunningham et...@hawaii.edu wrote:
Hello Freesurfer experts,
I have a question about how to determine if a covariate is important
Hello Freesurfer Experts,
I am currently trying to run the Linear Mixed Effects Models described in
the wiki here:
http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels
And I am running into difficulties that are fairly well described by the
last message in this previous mail thread:
like gray matter, but it could be damaged white matter
instead.
cheers
Bruce
On Tue, 19 Feb 2013, Eric Cunningham wrote:
hello freesurfer experts,
attached is an image drawn from the tutorial page.
http://surfer.nmr.mgh.harvard.**edu/fswiki/FsTutorial/**WhiteMatterEditshttp
Hi,
this link:
http://surfer.nmr.mgh.harvard.edu/fswiki/TalFailV5.1
discusses a solution to bad talairach.xfm transforms, the -use-mritotal
flag.
this link:
http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV
mentions that the talairach.xfm is used to calculate the total intracranial
volume.
is using
into
/apps/fs510/tktools/ (after making a copy of the one there).
doug
On 11/5/12 5:00 PM, Eric Cunningham wrote:
[e4fs@cluster bin]$ ls -l `which tkregister2.bin`
-rwxr-xr-- 1 jsadinol fs 21663433 May 22 2011 /apps/fs510/tktools/
tkregister2.bin
[e4fs@cluster bin]$ tkregister2 --all
Hi folks,
In previous threads, the command provided to check the talairach.lta is...
tkregister2 --mov $FREESURFER_HOME/average/RB_all_2008-03-26.gca \
--targ ../brainmask.mgz --lta-inv talairach.lta --reg
talairach.lta.reg.dat \ --surfs --s $subject
When I try to run this command, I run into
, but
most seem like they could be made better by a tweak here or there. At what
point would I just be adding randomness by manually editing?
About what percent of a given dataset would you expect to manually edit?
Much appreciated,
-Eric Cunningham
Hi Bruce,
I am running version 5.10
Thanks,
-Eric
On Wed, Oct 10, 2012 at 3:13 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
Hi Eric
what version are you running?
Bruce
On Wed, 10 Oct 2012, Eric Cunningham wrote:
Greetings,
I am trying to determine how bad a talairach.xfm
5.1 specifically has a problem with Talairach accuracy (is that
right Nick?). Should be much better with the next release
On Wed, 10 Oct 2012, Eric Cunningham wrote:
Hi Bruce,
I am running version 5.10
Thanks,
-Eric
On Wed, Oct 10, 2012 at 3:13 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
Hi,
I have a few very basic clarification questions regarding the recon-all
processing pipeline.
I am currently following the instructions here:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
Near the end of the page, it instructs me to rerun the whole process using
my new
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