a. You can map your seeds to the cortical surface of your subject (mri_vol2surf), then to fsaverage (mris_surf2surf), then view them on fsaverage. b. Not sure what you mean by this. The FC analysis just computes maps and those maps are compared at the second level. At that point it does not really matter how the maps were generated (ie, they could be FC, they could be task, they could be thickness, they could be PET).

On 05/13/2016 11:54 AM, Sahil Bajaj wrote:

Hello FS experts,

I am sorry for reposting this question in the forum:

I calculated subject-wise resting-state FC maps after defining seeds into subject-wise anatomical space as mentioned in the manual. Now, location of seed regions across subjects differ a little.

According to manual, FS maps the time-series on fsaverage lh and rh hemisphere. That means connectivity maps for each subject are registered to fsaverage space and it should be fine to calculate 2nd level maps.

If that's correct then my questions are: (a). How seeds can be overlaid on 2nd level maps or 1st level maps because seeds are not in fsaverage space but both 1st and 2nd level connectivity maps are. When I see subject-wise FC maps, those are little far from the actual seed locations which I defined in subject-wise anatomical space. (b). How FS deals with seed regions in terms of 2nd level analysis because it calculates FC from seeds which are in subject-wise anatomical space but it reports FC in fsaverage space, so 2nd level results are even more far away from actual seed region locations?

I would really appreciate any thoughts/suggestions on this.

Thanks, Sahil

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Sahil Bajaj Post-doctoral Fellow Nantz National Alzheimer's Center, Department of Neurology The Houston Methodist Research Institute (THMRI) Houston, TX, USA. E-mail:sahil.brain@gmail.com mailto:E-mail%3Asahil.phy@gmail.com

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