yes, that should be the most accurate. It computes the interior of the
white surface, excluding voxels that are not white (ventricle, thalamus,
etc....)
cheers
Bruce
On Mon, 15 Dec 2008, Christian Scheel wrote:
Thanks Doug, Nick and Marie for your great support!
With regards to what you wrote to Maartje about the total gray matter volume
I understand that the best way to measure it is using
mris_anatomical_stats -l ?h.cortex.label subject ?h
for every subject and every hemisphere. Maybe we should include this option
on the wiki page http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
I would be fine with updating this page.
For the total white matter volume I am still not 100% sure if it's the
command
mris_wm_volume subject ?h
which gives me the most accurate results. This command is recommended on the
same wiki page.
Best regards,
Christian
---
University of Cologne
Department of Psychiatry
Doug Greve schrieb:
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 the smoothing level to 15 or even 20, but is it really
appropriate to use such high levels of smoothing?
As with all smoothing, there is no real standard, but it is not unusual to
use 15 or 20. Surface smoothing is much more forgiving that volume
smoothing in terms of mis-localization of activation. In fMRI volumetric
analysis, it is not unusual to see 10-20mm smoothing.
2) In Qdec is there a possibilty to set something like an 'Extent
threshold' in order to display only clusters of a certain size and hide
all clusters that are smaller?
This is not possible in Qdec yet. Outside of qdec, there is mri_surfcluster
which will do this. We will be adding it into qdec.
3) Am I correct that the best way to get the total gray and white matter
volume is
a) for the gray matter volume:
mris_volume ?h.pial
minus
mris_volume ?h.white
b) for the white matter volume:
mris_wm_volume subject ?h
I'll leave this for others.
I read that the values for white and gray matter in the aseg.stats are not
that accurate, but what about the GrayVol value in the ?h.aparc.stats
files? I was a bit surprised that the sum of these GrayVol values is not
the same as the total gray matter volume calculated with mris_volume
(although it comes quite close)
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?
I'll leave this for others.
5) I have tried loading my data into the qdec version shipped with
Freesurfer 4.05 and noticed that now there is an option to chose between
DODS and DOSS. In my study I wish to compare the thickness of a group of
patients and a group of controls accounting for gender and age. Did I
understand Dougs freshly updated wiki page correctly and can I use DOSS in
case I assume that age has the same effect on patients and controls (so
same slope) and they are only starting at different thickness levels? And
when chosing DOSS is age really still in the calculation as a covariate? I
was surprised to see that I can only chose the question 'Does the average
thickness, accounting for gender, differ between patient and control' but
not 'accounting for gender and age'.
Yes, if you believe that the slope is the same for patients and controls,
you can use DOSS. Age is used as a covariate, and the question text should
be changed to reflect this.
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 do I just need the core programm?
I'll leave this for others.
doug
Any help is greatly appreciated.
Best wishes,
Christian Scheel
---
University of Cologne
Department of Psychiatry
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