On 5/11/13 7:41 PM, Tudor Popescu wrote:
Hi everyone, I resort to asking some questions here again, after
feeling increasingly stupid (maybe just tired) after reading the wiki
pages relevant for my analysis (ROI, thickness).
1) How should the contrast vector for a group comparison while
factoring out age and gender be built? I didn't quite understand the
example in the tutorial
<http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#Contrasts>based
on intercept/offset. In my case, shouldn't I have 4 elements in the
vector (group1, group2, age, gender), with the first two elements
receiving perhaps 1 and -1, since they are directly compared, and the
last two elements 0 and 0 since I am not directly interested in their
effect on the dependent variable?
Gender should be two groups (don't code it as a continuous variable).
This will give you 8 columns. g1, g2, male, female, g1-age, g2-age, etc.
2) Are the structures described in the .label files produced by
mri_annotation2label in common (MNI) or in that subject's individual
space?
Individual space.
3) For my thickness analysis, I have in mind an ROI for which I have a
set of centre coordinates from a meta-analysis of relevant functional
studies. What is the best way of defining the mask for this ROI as a
function of those coordinates, rather than taking the eponymous region
from the Destrieux or the Desikan atlas?
Assuming that the coords are in mni152, convert it to mni305 (to do this
search for "coordinates" on the wiki). Then load up fsaverage and find
the vertex closest to this coordinate. The draw a label around this vertex.
4) Exactly which of recon-all's outputs has to be inspected, for each
subject, in order to tell whether the surface reconstruction has gone
well?
Load up the surfaces over the nu.mgz or the T1.mgz and see if the
surfaces follow the anatomy properly.
5) Is it statistically correct to run the same design both with a DODS
FSGD and with a DOSS FSGD? It's not entirely clear to me what
assumptions each one (DODS, DOSS) makes of the data, and which one I
should select in my case.
The DODS allows for interactions between a continuous factor and a
discrete factor. Eg, the thickness-age slope could be different between
males and females, and you could detect this with DODS. With DOSS, there
is only one thickness-age slope for all groups, so there is no way to
detect an interaction.
doug
Thank you very much indeed.
Tudor
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
