the sig value is actually -log10(p)*sign(gamma) where gamma is the
contrast (gamma.mgh). The p-value is two-tailed, and the color indicates
what tail you are on.
doug
On 03/10/2015 01:21 PM, Matthieu Vanhoutte wrote:
Dear FreeSurfer's experts,
I have launched a GLM analyses following
Hi Bengi
yes, we've just started such a project but it will be some time before we
have anything usable.
cheers
Bruce
On Wed, 11 Mar 2015, Baran, Bengi wrote:
Dear FreeSurfer developers and users,
I’m wondering if any of you worked on further segmentation of the thalamus
into thalamic
I don't think so, but maybe Martin or Nick know otherwise. Otherwise,
you'll have to use mri_glmfit
doug
On 03/11/2015 04:47 AM, Gabriel Gonzalez Escamilla wrote:
Dear FS experts,
I'm wondering whether is possible to perform vertex analyses on pet
data using qdec, I'm running FS v5.3.0
It actually assumes that it changes sinusoidally. I don't have a
solution for a log change. Can you write a matlab line that describes it?
On 03/10/2015 07:31 PM, Jackie Lam wrote:
Hi all,
For Freesurfer’s retinotopy analysis, does it assume that the eccentricity
ring stimulus
Oh, I see what you mean. I accidentally sent you the within group analysis
script. I am attaching the first level analysis script now. I also labeled the
different steps to simplify the script a little bit.
From: freesurfer-boun...@nmr.mgh.harvard.edu
I checked registration before and it was fine. However, I'll go back and look
at the first value in the aslcal.reg.mincost file. What is the normal range?
Also, I don't understand what you mean with the FSL initialization fails and
try --init-spm - can you please give me some more information?
Try checking the individual registrations (or look at the first value in
the .mincost file) to find subjects whose registration may have been off
and so causes the final mask to be non-sense. Sometimes the FSL
initialization fails. If so, you might try it with --init-spm
On 03/11/2015 05:15
So you are comparing FDR correction against cluster-wise correction and
they are different? Why would you expect them to be the same?
On 03/11/2015 01:33 PM, Sofia Rodriguez Penuela wrote:
Dear experts,
I'm running surface thickness analyses with both command line and Qdec.
The
This is the script I am using to create cbf.talaraich.mgz (attached).
Thanks,
Rick
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, March 11,
Sure. I simplified it and attached it again. Please let me know if this is
helpful!
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, March 11,
I still can't really tell what it is doing. It looks like it is just
concatenating several input files that are passed on the command line.
how were those created?
On 03/11/2015 03:54 PM, Wolthusen, Rick Peter Fritz wrote:
Sure. I simplified it and attached it again. Please let me know if
Hi Doug et al.,
Here is the glmdir file you were requesting:
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1vzzxqva928
Thanks,
Rick
From: Wolthusen, Rick Peter Fritz
Sent: Tuesday, March 10, 2015 2:10 PM
To: Freesurfer@nmr.mgh.harvard.edu
Subject: RE:
Something went very wrong with your first level analysis because the
final mask is pretty messed up. how did you create cbf.talairach.mgz ?
On 03/11/2015 03:13 PM, Wolthusen, Rick Peter Fritz wrote:
Hi Doug et al.,
Here is the glmdir file you were requesting:
Hi all,
I have a nifti volume with activity that I want to edit so that it's a
mask for certain structures. I know how to draw in activity, but I
couldn't find a way to erase it in Freeview. Is there a way to erase the
values in a nifti volume?
If not, I can convert the nifti file to a .label
Hi,
I am getting a unexpected result when I am running optseq2 and I don’t know if
it is something I am not understanding correctly or if something else is going
on. It is with ITI times. If I understand correctly the psdwin I entered below
should return a min time of 4 and a max of 10, but I
Dear FS experts,
I'm wondering whether is possible to perform vertex analyses on pet data using
qdec, I'm running FS v5.3.0 under ubuntu 12.04. I have all my functional data
converted to surfaces.
Qdec 1.5 says that the functional design is not yet implemented. So, I'm
wondering is there is
For the range, lower is better, but it impossible to say exactly what is
good enough because it depends on your data. If it is 0.8 or higher,
then that is probably bad. What I'm hoping is that there will be one or
two outliers. The --init-spm was in place of --init-fsl in bbregister.
But you
Hi everybody
I was looking at my subjects and I noted that the superior occipital region is
labeled as superior parietal cortex in the aparc parcelation.
Then I discovered that the bert subject, that comes as reference with
freesurfer, and that the fsaverage also have their superior
Hi Kate,
if you are only running stats on the longitudinally processed dirs, it
should be sufficient to copy only the *.long.* directories and the base
directories. You can skip the cross sectionals.
If you do an LME, you can probably also skip the base dirs. But you'd
need them for the
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