Dear FSL users,
I am working on resting state data and calculating seed-based functional connectivity maps, and I am observing some weird results in the maps. There is a layer-behavior in the maps, and layers seem to correspond to slices. Please see the image attached.
At first we suspected that wrong slice timing correction is the culprit (there was a post on these boards about a similar problem some time ago), but I have tried without slice timing correction and with different settings, e.g. using slice order or the exact slice timing information from the header, using first or middle image as a reference, but this didnt fix the problem. Are there other possible reasons for such behavior?
The EPI data is acquired at 3.5mm iso resolution with interleaved slices, the data is slice-timing and motion corrected, then detrended, filtered and covariate-regressed (6 motion parameters, WM and CSF, global mean) all in its native space. Then it is registered to individual T1 images, where certain ROIs are generated with FreeSurfer, and seed-based connectivity analysis is performed using steps outlined here http://www.fmrib.ox.ac.uk/primers/rest_primer/4.1_SCA/index.html.
Also, examining the original EPI data, i.e. not preprocessed in any way, some datasets also exhibit slice intensity differences in some volumes. It is not consistently across all volumes, and only very few subjects have it, much fewer than have this behavior in connectivity maps.
All of your insights would be greatly appreciated.
Best regards,
Renat.
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