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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