Bruce,
You had posted that there is a 'backwards compatibility flag' regarding control
points manually specified to the aseg normalization in Freesurfer version 5.1
(see your thread from 1/27/12 below). You said that Nick might know about this
flag.
I too had noticed very different behavior
Dear Freesurfers,
I know that Qdec outputs coordinates in a "Freesurfer specific space", rather
than in Talairach space, per this old thread
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2008-November/008878.html
However, I found that mri_surfcluster (Freesurfer v5.0) in its summary out
For a two factor GLM analysis with two levels, I'm uncertain as to why the
Freesurfer GLM measurement of the interaction effect of say, group and gender,
is a t-test and not an F-test. In my case, my factors are group (healthies vs
patients) and gender (male vs female). For a 2x2 two-way ANOVA a
the Folding Index (?).
Hope it helps,
Marie
On Mar 9, 2011, at 3:56 PM, Chris Hyatt wrote:
> I had asked the Listserv a week or so ago if there was a way to get the
> Folding Index measurement for each subject and ROI using aparcstats2table,
> similar to area, thickness, gray vol
I had asked the Listserv a week or so ago if there was a way to get the Folding
Index measurement for each subject and ROI using aparcstats2table, similar to
area, thickness, gray volume etc.. The data are in the ?h.aparc.stats files for
each subject, along with thickness, thickness std, surface
Hi all,
I'm trying to extract the folding index for each subject/hemisphere/roi from
?h.aparc.stats into a single table with all subjects. It appears though that
aparcstats2table will only extract area, volume, thickness, thicknessstd and
meancurv, not folding index, even though these values a
You have /stat/ rather than /stats/ in the address. Have you checked that?
>>> Alex Hanganu 2/24/2011 12:22 PM >>>
Dear Chris, Doug,
We created a ROI in qdec (EXMPL.label) and tried to measure it's thickness.
The cmd used:
aparcstats2table --hemi ?h --subjects 1 2 3 --parc .../DIR/EXMPL.label
hemisphere is say, 15.294 mm, does mri_glmfit-sim (mc-z) use interpolated data
from fwhm15/ and fwhm16/ in its calculations, or does it choose the nearest
value (in this case, fwhm15)?
Thanks,
Chris Hyatt
Olin Neuropsychiatry Research Center
Institute
I've read both Hagler et al 2006 Neuroimage (Smoothing and cluster thresholding
for cortical surface-based group analysis of fMRI data) and B. Douglas Ward's
description of AlphaSim that both describe clusterwise correction for multiple
comparisons.
I recently found, however, an MGH Freesurfer
Dear Freesurfer users,
I am using mri_glmfit-sim to do clusterwise correction for multiple
comparisons. I ran the Z Monte Carlo simulation for 5000 iterations for my 43
subjects (vertex wise threshold of 2.0 or p < 0.01), but I received different
results than when I ran the correction using the
Hi,
In a recent Freesurfer mailing list question, someone asked how they could
correct temporal lobe intensity normalization problems for a large number of
subjects without having to add control points for every subject (very time
consuming).
The recommendation from Bruce Fischl was:
" On
0 minutes.
>
> Alex Zaitsev
>
> Chris Hyatt wrote:
>>
>> We recently installed a Dell Blade server cluster running Freesurfer
>> v4.5 under CentOS 64-bit Linux, with each Blade server having two
>> Intel Xeon E5405 quad core CPUs, running at 2.0 GHz, 2x6144 KB cach
We recently installed a Dell Blade server cluster running Freesurfer v4.5 under
CentOS 64-bit Linux, with each Blade server having two Intel Xeon E5405 quad
core CPUs, running at 2.0 GHz, 2x6144 KB cache and 16 GB of RAM, with a swap
file of size between 8-16 GB.
Using a single Blade server of
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