Hi Michael,
I can answer the subfield part - perhaps someone else (Bruce?) can
chime in regarding aseg.
For the subfields, there isn't really a standard routine to go in and
alter the segmentation results. You could try to alter the aseg
hippocampus segmentation as this is what is used to
Dear statistic experts
We have done statistics between two independent groups using an independent
t-test. One group consistent of 13 male patients and the other group
consistent of 13 male control subjects who were matched to the patients with
respect to age and education (in years).
The
Please, could anyone let me know how to perform statistical analysis in QDEC to
look at the interaction between two genes on cortical thickness?
Vincenzo Pierro
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Please, could anyone let me know
how to perform statistical analysis in QDEC to look at the interaction
between two genes on cortical thickness?
Vincenzo Pierro___
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Freesurfer@nmr.mgh.harvard.edu
Hi Michael
we have seen that occasionally, but that looks like a pretty bad example.
If you upload the subject I'll take a look. We have some unreleased tools
that can help with this (a relatively small manual intervention).
cheers
Bruce
On Mon, 23 Jul 2012, Murray, Michael wrote:
Dear all,
After studying the freesurferstats2table script for a while, I think I figure
out what these surfaces are. Below is my understanding. Please correct me if I
am mistaken!
In the aparc_area_lh.txt, the surface area should be one based on the pial
surface, not the white surface,
Hi Daniel
sorry, I meant to respond to your previous post. We generate statistics
for both the white and pial surfaces. For historical reasons the ones
without specific surface name in them represent the white surface (i.e. the
pial ones will all say pial). We can produce both Gaussian and
Hi Bruce,
Thanks for the correction!
So according to your email, the correct interpretation should be,
In the aparc_area_lh.txt, the surface area is one based on the white
surface, not the pial surface, based on the historical naming.
In the aparc_meancurv_lh.txt, the mean curvature is one
yes, that's right
Bruce
On Tue, 24 Jul 2012, Yang, Daniel wrote:
Hi Bruce,
Thanks for the correction!
So according to your email, the correct interpretation should be,
In the aparc_area_lh.txt, the surface area is one based on the white
surface, not the pial surface, based on the
Hi Jurgen, I don't think it is too unusual to do this kind of thing, ie,
a paired test where pairing is based on gender, age, and education, but
you know your data and field better than I do. It is not the case that
one is more conservative than another (they are the same) assuming that
the
Those are the values I mentioned before (lhCortex, etc, see below). I
don't understand your concern about the deep structures.
doug
ps please remember to post to the freesurfer list and not to me
directly. thanks!
On 07/24/2012 06:56 AM, Emelie Andersson wrote:
Thank You for your answer.
I
Set up each gene as a discrete factor, then look for a difference.
doug
On 07/24/2012 08:56 AM, Vincenzo Pierro wrote:
Please, could anyone let me know how to perform statistical analysis
in QDEC to look at the interaction between two genes on cortical
thickness?
Vincenzo Pierro
Hi Jurgen,
I actually just came across a similar situation in which I tried to
convince my PI that a paired t test is more appropriate. In my humble
opinion, if you are applying an independent group test, than the matching
design is irrelevant in this analysis because you're not taking any
Hi:
How much memory needs tracula to process a DTI study ?... Because my
PC (Ubuntu Linux, 4GB RAM) exit because it can't allocate memory in
trac-preproc... There exist any tip trick in such a case?...
Sincerely,
--
Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Hi Ed, the problem appears to be with the initialization. For some
reason, fslregister is not initializing this data well. I don't know why
the call directly to flirt works (and I've verified here that it does).
When I initialize by hand or with SPM, bbregister works fine with the
standard
Hi Doug,
Yes, sorry about that! I realized after I'd sent the email to you that I
should've sent the email to the freesurfer list as well.
We were hoping to look at volume in subcortical regions of the brain --
basal ganglia, hippocampus, amygdala, etc. Do know if there are commands
to do the
Hi Alex, do you want to do it on an ROI basis? If so, you can use
asegstats2table to create a table of your subjects at the two time
points, then import this table into SPSS. Or you can run the table
through mri_glmfit to do the paired-t analysis.
doug
On 07/24/2012 01:56 PM, Alexandra Tanner
Hi Gonzalo - You'll find some recent emails on this in the archives. In
short, you can try deleting a few lines from the file:
$FREESURFER_HOME/trctrain/trainlist.txt
For every line you're deleting, you're removing a subject from the tract
atlas that tracula uses. There are currently 33
A paired t-test is a special case of a repeated measures ANOVA with a single
within-subject factor and two levels. You should use it when the measurements
in one group are correlated with the measurements in the other group and there
is a within-subject effect that persists across paired
Hi Doug,
We don't want to do ROIs because we're trying to get a thickness map of
the entire subcortical region of the brain.
Prior to trying this, we ran a within subjects paired analysis that gave
us thickness maps of cortical surface. We ran these commands to look at
the thickness maps in each
Hi Alex, what do you mean by a thickness map of the subcortical region?
The subcortical structure are usually characterized by simple volume
measurements (eg, hippocampus has a volume of XXX mm3). There are tools
out there to do voxel based morphometry. Is this what you mean?
doug
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