Hi Doug,
thanks for your answer. My commands are:
mri_mcsim --o $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/labelname \
--base mc-z \
--surface fsaverage lh \
--nreps 1 \
--label /path/to/label/lh.labelname.label
mri_glmfit --C /path/to/contrast/
No; it is not thickness; it is GM/WM intensity values;
thank you for the suggestion with mri_mcsim.
2015-03-23 18:22 GMT+01:00 Douglas N Greve :
>
> Yes, 35 is more than I've precomputed. But another question is whey it
> is 35 when it looks like you've smoothed it by only 15. What is the
> nat
>
> Dear FreeSurfer,
>
> I edited the pial surface based the instruction in the following page:
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview
>
> After I removed the dura, I ran this commend:
>
> recon-all -autorecon-pial -subjid pial_edits_before(with my own subject)
>
Yes, 35 is more than I've precomputed. But another question is whey it
is 35 when it looks like you've smoothed it by only 15. What is the
nature of this data? Is it thickness?
If this is something you really need/want to do, I'm recommending that
people start using mri_mcsim instead of runnin
Yes,
the mri_glmfit run correctly (also for a similar analysis where the
computed FWHM was under 30 mri_glmfit-sim run without problems)
the mri_glmfit command was:
*mri_glmfit --glmdir $path/resultsDIR --y
$path/lh.all_long.wm_orig_0.2.mgh-rate.fwhm15.fsaverage.mgh --fsgd
$path/gender_csf_stroop
It is in -log10(p). There will be the vertex number for the max in that
file. You can load up the F.mgh file to get the F-value for that vertex.
Assuming your contrast matrix only has one row, then t = sqrt(F). You
can compute the z-value in matlab. first convert the -log10(p) to a
p-value wit
Is there not a BV template that you can run through recon-all? That will
make things much simpler. Otherwise, you'll need to convert the
coordinates to something that FS understands which is going to be a real
pain. See here form more info
http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSy
You can run mri_annotation2label on the a2009s annotation. The label
file will have a list of vertices and their XYZ coordinate.s They are in
"tkregister" space of the conformed anatomical. See
http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 03/19/2015 04:52 AM, Santosh Yadav wrot
We don't do BG functional segmentation (FS segments it into putamen,
pallidum, caudate, and nucleas accumbens). We have partial volume
correction software coming out in version 6. We also have kinetic
modeling using MRTM1 and MRTM2 in version 6.
doug
On 03/18/2015 12:55 PM, FV SCHRAML wrote:
Use the result from mri_glmfit.
doug
On 03/20/2015 10:20 AM, Egil Nygaard wrote:
>
> Dear Freesurfer support,
>
> I find the qdec to be very pedagogic in its outlay, and would love to
> use it. However, I find several discrepancies as compared to results
> from the mri_glmfit analyses, and wonde
I don't use SPSS so I can't really comment with any authority. But I
think it is group*gender and group*gender*age
doug
On 03/20/2015 10:08 AM, Egil Nygaard wrote:
>
> How are the DODS analyses in Freesurfer comparable to interaction
> terms in GLM analyses in SPSS? I notice that others have ha
At that point, it is the same as doing a group thickness or fMRI task
analysis (FC measure per vertex instead of thickness or task). Look in
the task-based fsfast tutorial.
doug
On 03/22/2015 10:23 AM, Barbour, Tracy,M.D. wrote:
> Hello,
>
> I am doing functional connectivity analysis using the
did this run correctly with just mri_glmfit? What was your mri_glmfit
command line? Why are you running a simulation instead of using cached data?
doug
On 03/21/2015 10:52 AM, Dídac Vidal wrote:
> Dear Freesurfer users,
>
> I am trying to run mri_glmfit in simulation mode as the computed FWHM
Hi,
I’m trying to checkout a copy of the open source repo and getting a CVS
read lock error.
$ cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot
checkout -P -r release_5_3_0 dev
cvs checkout: failed to create lock directory for `/usr/fscvsroot/CVSROOT'
(/usr/fscvsroot/CVSROOT/#cv
The format of the fsgd file looks ok, but I suspect that there is a
platform issue. How did you create it? Under windows? You can try
something like
cat your.fsgd | sed 's/\\r/\\n/g' > new.your.fsgd
use new.your.fsgd and see if this fixes the problem.
On 03/20/2015 02:48 PM, Elrod, Christian
Can you send your mri_glmfit, mri_glmfit-sim, and mri_mcsim command lines?
On 03/20/2015 02:24 PM, Janosch Linkersdörfer wrote:
> Hi all,
>
> I have a question/problem related to restricting monte carlo cluster
> correction to a reduced search space.
>
> I have:
>
> 1) created a label including
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