Dear all,
I have got several questions about the analysis of my data. Maybe you
can help me out:
1) Regarding the different levels of smoothing (FWHM) in Qdec are there
already some 'standards' that one should usually stick to? My results
look better when I set the smoothing level to 15 or e
Hello,
I forgot to mention another query regarding recon-all -make all:
If I do end up running this command on the subjects that fail the qcache
processing (so effectively rerunning the whole recon-all stream), will
any edits I have made to fix errors (such as control points, wm.mgz
edits and
Hi,
I'm using paint-sess to create .w files from a contrast's sig map (I need
the .w files for use with MNE).
When I view the sig.nii file in tksurfer, the activation differs subtly
but noticeably from the .w files.
For example, I'll run a command like:
paint-sess -analysis EC -contrast eVc -off
I just noticed this about a week ago and have not been able to track it
down. The w file (or anything created by mri_vol2surf, which is run by
paint-sess) is the gold standard. When tksurfer loads in a
volume/registration, it is slightly off. I'm working on why.
doug
Jesse Friedman wrote:
H
Hello,
I've noticed a behavior in QDEC (v1.1 under FS v4.1.0) that appears to
be a bug regarding the "slopes" output to the terminal, and the
corresponding regression lines displayed in the scatterplot, when using
more than one continuous covariate.
I ran an analysis on cortical thickness on a g
Christian Scheel wrote:
Dear all,
I have got several questions about the analysis of my data. Maybe you
can help me out:
1) Regarding the different levels of smoothing (FWHM) in Qdec are
there already some 'standards' that one should usually stick to? My
results look better when I set th
Hi Tricia,
If you have nice cortical reconstructions, there should not be any
consideration in calculating the lGI, it will be done automatically
and will not need any special change (except if you want to try with
different radii). However, you are right that there is a certain
extent o
Hello,
What is the role of the spatial AR1 that is automatically computed as
part of a QDEC analysis?
thanks,
Mike H.
--
Michael Harms, Ph.D.
Conte Center for the Neuroscience of Mental Disorders
Washington University School
it is automatically computed by mri_glmfit and used to compute the fwhm
(saved in fwhm.dat). I'm working on an RFT-based correction for multiple
comparisons correction, and that requires fwhm. You also need it if you
are going to use the monte-carlo-based simulation.
doug
Michael Harms wrote:
Marie,
Are any special toolboxes required in Matlab to run the lgi code? Or
will plain matlab suffice?
Nick
>
> 6) I would like to have a look at the local gyrification index aswell
> but still need to buy Matlab for it. Do I also need some extra toolboxes
> to run the lgi calculation - or
Christian,
as long as all your subjects were recon-all'd using the same version
(4.0.2), then you can use qdec and mri_glmfit from 4.05 or 4.10.
Nick
>
> 4) All of recon-all has been run with Freesurfer 4.02 for all subjects -
> is it OK to use Freesurfer 4.05 or 4.10 for the analysis?
> Best
Rysia,
Your edits will be maintained. Edits are deleted only if you include a
-clean flag (like -clean, or -clean-aseg, or -clean-wm, etc).
Nick
On Thu, 2008-12-11 at 15:25 +, Burmicz, Ryzarda wrote:
> Hello,
>
>
>
> I forgot to mention another query regarding recon-all –make all:
>
>
Rysia,
btw, there is a flag you can run in recon-all to check if the vertex
numbers on all the files are the same:
recon-all -s subjid -vno_match_check
it calls the script vno_match_check, which is a handy qa tool.
Nick
On Thu, 2008-12-11 at 15:18 +, Burmicz, Ryzarda wrote:
> Hello,
>
>
Alexandru,
I can't say i've seen this done before, but i think what you would do is
use mri_surf2vol to map the sig.mgh file back into your subject volume
space. you would need a register file to do this, but it is included
with a standard freesurfer recon. that is, the surface data is on the
'f
Saud,
Which version of freesurfer was installed? What OS do you have?
Nick
On Wed, 2008-12-10 at 16:09 +, Saud Alhusaini wrote:
>
>
> -- Forwarded message --
> From:
> Date: Wed, Dec 10, 2008 at 4:08 PM
> Subject: HELP!
> To: saud.alhusa...@gmail.com
>
>
> You are not
Mike,
That button operation was changed to make things 'easier', but I'm dont
like it that way either. I think I'll make it configurable in a future
release. There is no way to turn that off in the current release (i
just put that scatterplot window behind the main window and luckily it
doesnt g
Maartje,
You can get total gray matter volume for a hemi with this:
mris_anatomical_stats -l ?h.cortex.label nick12 ?h
replacing ?h with lh and rh. the label file causes it to exclude the
non-cortical region (medial wall including corpus callosum) to give the
most accurate measure. you'll have
Marie,
Thanks for the info. I just updated the page:
https://surfer.nmr.mgh.harvard.edu/fswiki/LGI
Nick
On Thu, 2008-12-11 at 23:25 +0100, Marie Schaer wrote:
> Nick,
>
> To run lGI, one need Matlab with the image processing toolbox
> installed. Maybe we can add this info in the lGI wikipa
Hello,
I'm curious, what algorithm is used for setting the "mid" and "max"
threshold values in QDEC when using the "Set Using FDR" button?
And, what does the algorithm do for setting the "min" threshold when no
single p-value is significant enough to satisfy the necessary inequality
for the speci
Hi surfers,
I am trying to understand the source of the following errors. I know it was
not able to locate libXss, but why
should mris_volmask need libXss ? I have been told it is a library used by X
sceensaver
mris_volmask --label_left_whit
Sid,
I don't know why, but apparently libvtkHybrid.so.5.2 and
libvtkRendering.so.5.2 use it (as discovered by running ldd upon all the
mris_volmask.bin lib dependencies).
What platform are you running? Probably VTK would need to be built on
that.
Nick
On Thu, 2008-12-11 at 16:27 -0800, Siddh
Hi Nick,
it is x86_64 GNU/LInux . The ldd i did did say that vtk
libraries were not found.. i will remember to check them more throughly
on subsequent runs...
thanks
sid.
On Thu, Dec 11, 2008 at 5:36 PM, Nick Schmansky
wrote:
> Sid,
>
> I don't know why, but apparently libvtkHybrid.s
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