use
> mri_segstats something like
>> mri_segstats --i $SUBJECTS_DIR/fsaverage/surf/lh.white.avg.area.mgh
>> --seg glmdir/mask.mgh --id 1 --accumulate --sum sum.dat
>>
>> doug
>>
>> On 10/29/15 5:10 PM, Jeni Chen wrote:
>> > Hello,
>> >
>
Hello,
When running the Clusterwise Correction for Multiple Comparisons, I used a
label as a mask to restrict search area. I want to find out the size of that
label, so I guess I can pull that information out from the "mri_glmfit.log",
specifically under 'searchspace'? Also I only see a numeric
Hi,
Just wondering if the periaqueductal gray is part of the automatic segmentation
process and if we can obtain the volume. I checked the aseg table but didn't
see it, however, I somehow remember seeing it before... Was it ever included?
Thanks.
Jeni
__
econ tools, and if I install the latest
FS, I will have to rerun the preprocessing... So is it possible to install the
latest Freeview separately?
Thanks.
Jeni Chen
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.
;
On 2013-04-25, at 5:55 PM, Jeni Chen wrote:
> Hi Doug,
>
> The very first command line was:
>
> mri_glmfit-sim \
> --glmdir
> /Volumes/RainvilleHD2/Imaging_Data/Thickness/MATHIEUP_IBS/FS_1stAnalysis/GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS
> \
> --sim
t 5:30 PM, Jeni Chen wrote:
> The original command line:
> > mri_glmfit-sim \
> > --glmdir GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \
> > --cwpvalthresh .999 \
> > --no-sim
> > GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS/csd/mc-z.abs.3.j001-1GroupAvg-Cor-thickne
t-sim \
> --glmdir GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \
> --cwpvalthresh .999 \
> --no-sim 1GroupAvg-Cor-thickness-Mod-VAS
And it did not work either.
Thanks.
jeni
Douglas N Greve Thu, 25 Apr 2013 14:08:32 -0700
> what was your orignal mri_glmfit-sim command line?
On
o track
down the problem. Also, please include previous correspondence. We
answer a lot of emails here, and the easier you make it on us, the
faster we can solve your problem.
thanks!
doug
On 04/25/2013 04:41 PM, Jeni Chen wrote:
> Thansk Doug. I tried it but still doesn't w
Thansk Doug. I tried it but still doesn't work. Any other thoughts?
jeni
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the p
Hello,I was trying to run mri_glmfit-sim at a lower cwpvalthresh so I specified the --no-sim option to avoid re-running the entire simulation again. I entered my DSC file but in the end I get the error message: "cannot find any csd files". Here is what I entered:mri_glmfit-sim \--glmdir GLMFIT/LH_1
Phew! Thanks!
jeni
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e
Hello,
Just a quick question, if the 'cwpvalthresh' flag wasn't specified when running
mri_glmfit-sim, the script will use the default .05 value, correct?
Thanks for clairfying.
Jeni Chen
___
Freesurfer mailing
Hello again,
In Qdec we get a plot of the data for a particular vertex showing the variable
and the thickness in the x, y axis respectively. Is there a way to get the same
plot when using glmfit? Where do I find the data for the plot? Thank you!
Jeni Chen
So essentially the -fwhm option in mri_glmfit does the same thing as
mri_surf2surf --fwhm ? Just want to make sure... Thanks again!
Jeni
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/free
does it
mean I'm 'double' smoothing my data?
Jeni
---
Jeni Chen, M.Sc.
Agente de recherche
Laboratoire de recherche en neuropsychologie de la douleur
Pav. Paul-G. Desmarais, Université de Montréal
CP 6128, Succ. A, Montréal, QC H3C 3J7
Tel: 514-343-6111 x4359
__
Hello Freesurfer experts,
I've been trying to figure out a way to run a directed search in a group
analysis. I read the tutorial on ROI analysis and some of the posts here, but
we can only do it with individual subject. Simply pout, I want to restrict my
search areas to 4 ROIs (determined from
Hi,
I was recently at the FreeSurfer workshop in Boston and learned about the
"Freeview" tool in Freesurfer. However, when I tried to run it from my own
laptop (Mac book pro), it crashes and gives the error message: "Bus error". I
didn't get a chance to have this problem solved while I was the
Hi,
I have 2 questions regarding Qdec:
1. We would like to save the results of 'cluster stats' (the printout on the
terminal after pressing the "Find clusters and go to max" button) to a text
file. Is there a way to do that? Or is it automatically saved in somewhere and
where would that locat
Hello Everyone,
I'm wondering if someone could post how to assign multiple cores to the
virtual machine in the VirtualBox Ubuntu version of FS. I saw an earlier
post that mentioned it but did not say how they did it. Basically
we have an Intel i7 with 4 cores and 12GB of RAM. When I installed
19 matches
Mail list logo
