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#Contrastsbased 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?
2) Are the structures described in the .label files produced by mri_annotation2label in common (MNI) or in that subject's 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?
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?
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.
Thank you very much indeed.
Tudor
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).
- 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#Contrastsbased 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.
- Are the structures described in the .label files produced by
mri_annotation2label in common (MNI) or in that subject's individual space?
Individual space.
- 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.
- 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.
- 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
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Douglas Greve -
Tudor Popescu