Hi,
Can you give me a reference to the method used for the
clusterwise correction for multiple comparisons (CSD)?
Is it Hagler et al, NeuroImage 2006, vol 33, 1093-1103?
Cheers,
Ed
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Hi Freesurfer Experts,
In my design i want to use a general linear model tot relate cognitive
performance and cortical thickness. I want to control for age, total gray
matter, gender and education. I have two discrete variables, including gender
(0,1) and Education (1-7). The problem is
Hi Doug,
I deleted all old analyses manually, switched to 5.1, redid
mkanalysis-sess, mkcontrast-sess, and selxavg3-sess, and still have
zeros in the most significant voxels.
If there was a bug fix in the meantime, could you please let me know
where to obtain it?
The version numbers are the
Dear freesurfer users,
I have a question regarding the kvlQuantifyPosteriorProbabilityImages command
to quantify hippocampal subfield volumes. Are all voxels with a probability
value bigger than 0 counted? Or is the command applying any threshold for the
estimation?
I have transformed the
Dear freesurfers,
I am doing retinotopy analysis using freesurfer 5 with
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis .
I have four runs, two eccen and two polar. For each run I have 15 seconds
fixation, 300 seconds stimuli and 15s fixation at the end (total 330s
Hi Negar, I cannot reproduce this error. I'm not sure how to proceed,
but here are three possibilities:
1. Is this a virtual machine? If so, do you have a real machine you can
run it on?
2. You only have 2G of memory on your machine. Can you increase that or
run it on a machine with more?
You'll have to run mri_vol2surf on each one separately to bring it into
the fsaverage space, then mri_concat to stack all of the maps into one
file. At that point you can compute a mean (also with mri_concat).
Generally, one does not do group analysis on sig maps though.
doug
On 11/27/2012
Can you send the full terminal output?
doug
On 11/27/2012 05:55 PM, Zhou, Wei wrote:
Hi Doug,
Thank you for reply. yes all 4 are in bold separately.
I tried -run-wise with selxavg3-sess, but it failed with the following msg:
Saving X matrix to
Oh, I did not realize this was an fsfast issue, I thought you were using
mri_glmfit. In that case, I'm not sure what could be causing the problem
since the p-values are being computed by matlab. How many runs do you
have? Is is a contrast that has a huge amount of power(eg, something vs
Hi Angela, Marie is the best one to answer the questions about
gyrification, but I've tried below
doug
On 11/28/2012 11:30 AM, angela.fav...@unipd.it wrote:
Hi all,
I would need some information about the local gyrification index.
I run the analyses and found which are the average indices
If you want to do it that way (assuming group1=1, group2=2, etc), then
the contrast would be
-0.5 0.0 0.5 0 0 0 0 0 0
This looks a little odd because it ignores group2, but that is the way
the math works out. I would probably use one group and use 1, 2, 3 as a
third covariate
doug
On
yes, reference hagler
doug
On 11/29/2012 04:52 AM, Ed Gronenschild wrote:
Hi,
Can you give me a reference to the method used for the
clusterwise correction for multiple comparisons (CSD)?
Is it Hagler et al, NeuroImage 2006, vol 33, 1093-1103?
Cheers,
Ed
Hi Doug,
Thanks for the response! Just out of curiosity, what map is typically used
for group analyses? Should I have used a map other than sig on the
individual subject level as well?
Thanks!
Alex
You'll have to run mri_vol2surf on each one separately to bring it into
the fsaverage space,
Hi Stan,
you cannot put discrete variables in the nuisance screen. I don't think
you can do this analysis from qdec since it contains discrete variables
with more than 2 levels. You'll need to use the command line stream,
ie, create an FSDG file, run mris_preproc, and mri_glmfit. See the
Hi Wei, the argument to -retinotopy should be the period of stimuluation
(ie, how long it takes the wedge to go around 360 degrees), not the
duration of your run. Also, it is not set up to handle fixation at the
beginning or the end, so you might want to cut those frames out.
doug
On
Usually the contrast effects size (ces) (in SPM this is the CON image,
in FSL it is the COPE image). Univariate maps are usually passed up to
the group level (the conjunction done with mergecontrasts is multivariate).
doug
On 11/29/2012 01:05 PM, Alexandra Tanner wrote:
Hi Doug,
Thanks for
Hi Doug, hi Caspar,
which matlab version are you using? We had some issues in the past that some
matlab 2007 and 2009 statistics toolbox versions returned p values of 0, which
obviously will not work as overlay, since those typically assume a volume of:
-log10(p_value)
and on matlab 2007b
Hi - thanks - I was thinking about doing it the other way (3 separate groups)
because as well as looking to see whether there is a linear change in dependent
measures (eg area) across groups I also want to see if there is a linear change
in the slope of dependent measure against age across
Yes, better powered, and it uses all the data. Otherwise you throw out
group 2. You can do the same thing with the other covariates (ie, scale
group1's age by 1, scale group2's age by 3, etc)
On 11/29/2012 02:58 PM, Mahinda Yogarajah wrote:
Hi - thanks - I was thinking about doing it the
Hi all,
I've installd FreeSurfer through Xubuntu virtual machine on Windows 7, 64
bit according to the installation instructions the FreeSurfer Beginner's
Guide. Unfortunately I'm facing an error in the recon-all process (as
described below), which I think has to do with the VM, because the
Thanks for the clarification! So I will rerun mergecontrasts-sess using
the ces image on my subjects and then run mri_vol2surf and mri_concat to
get the group map. Thanks for your help!
Best,
Alex
Usually the contrast effects size (ces) (in SPM this is the CON image,
in FSL it is the COPE
Hi - sorry probably being slow - not sure i follow - treating them as one group
(with appropriate covariate scale for level of endogenous factor/severity of
disease) and using scaled age scores how would i look for an interaction
between age and severity of disease across the group as both
Hi Doug,
Thank you very much. I have thrown all the fixation sessions and run the
analysis again. So in rtview how can i get the color scale bar which indicates
the corresponding time points of polar or eccen? Is it still supported in free
surfer 5?
Best
Wei
---
Hi
For volumes, I usually cite:
Forman, S.D., Cohen, J.D., Fitzgerald, M., Eddy, W.F., Mintun, M.A.,
Noll, D.C., 1995. Improved assessment of significant activation in
functional magnetic resonance imaging (fMRI): use of a cluster-size
threshold. Magn. Reson. Med. 33, 636–647.
It's also referenced
Hi Alex, unfortunately, you cannot compute a conjunction with the CES.
That's the problem with trying to do group-wise multi-variate analysis.
Another thing you can do is to do a group analysis with each contrast
separately, then do a conjunction of the group sig maps.
doug
On 11/29/2012
Hi Wei, I don't think I understand your question. Can you elaborate?
doug
On 11/29/2012 04:06 PM, Zhou, Wei wrote:
Hi Doug,
Thank you very much. I have thrown all the fixation sessions and run
the analysis again. So in rtview how can i get the color scale bar
which indicates the
Oh, sorry, if you want an interaction, then you would keep the age
covariate and add a covariate which is age*severity, then test that
covariate
doug
On 11/29/2012 04:04 PM, Mahinda Yogarajah wrote:
Hi - sorry probably being slow - not sure i follow - treating them as one
group (with
Hi Doug,
Thank you for your patient. I wanted to see how the polar angle correlates with
the map and I expect a wheel bar which distinguish different polar angles.
I typed:
rtview --s SUBJ1 --lh --polar --real
SUBJ01/bold/rtopy.self.lh/polar/real.nii.gz --imag
Those values are radians. Does that help?
doug
On 11/29/2012 06:09 PM, Zhou, Wei wrote:
Hi Doug,
Thank you for your patient. I wanted to see how the polar angle
correlates with the map and I expect a wheel bar which distinguish
different polar angles.
I typed:
rtview --s SUBJ1 --lh
I see. Yes. Thanks a lot.
Best
Wei
Those values are radians. Does that help?
doug
On 11/29/2012 06:09 PM, Zhou, Wei wrote:
Hi Doug,
Thank you for your patient. I wanted to see how the polar angle
correlates with the map and I expect a wheel bar which distinguish
different polar angles.
Hi Bryon - It does look like this individual and the tract atlas are not
in good alignment. The one step that requires good alignment is for
choosing an initial guess for the pathway. If the fmajor from all or most
of the subjects that are included in the tract atlas goes through the
Excellent, will look into it. Cheers Nick.
On 29 November 2012 04:58, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote:
Hugh,
That fix is described in the Known Issues section of 5.1 on the Release
Notes page:
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
look for the section
Dear Anastasia,
Thanks for your response. I have sent a subject that the problem in forceps
minor persists.
What I have done so far was to re-run the pipeline with reinit=1, check
the eigenvectors, increase control points, switch off brain anatomical mask
in dmric. It made the tracts look better
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