Hello, FSL experts,
Here's a question that came up today and that may change completely the way I've been analyzing my fMRI data with FEAT. Considering an analysis pipeline in which a 2nd-level analysis is *never* performed (e.g. individual differences study), we know that:
i. After completing the 1st-level FEAT analysis, a filtered 4D file is created. This file is in the same (typically low-res, 3x3x3mm for example) space as the original data, so no registration is applied at this point. (by the way, is the filtered data motion corrected?)
ii. Registration files are saved inside the /reg directory. If you manually apply these transformations to the filtered data, it will be registered to the space chosen as "Standard space" within the Registration tab in FEAT. If the high-resolution anatomical volume was chosen as the Standard Space, the filtered data will be upsampled to a higher resolution.
iii. Stat files are saved inside the /stats directory. Take tstat, for example. This is a 3D file, where each voxel is aligned with the motion-corrected filtered data, but still in the low-resolution space.
Now, let's suppose you define some masks in the low-resolution space, based on tstat maps you got from one scan. You want to apply this mask onto tstat maps from other scans. My questions, then, are:
1) Can you apply the same mask to tstat maps from different scans? In other words, are tstat maps voxels, from different scans, aligned between each other?
2) If not, what do I need to do if I want to apply a single mask to 1st-level tstat maps from different scans? I don't want to upsample my data to the standard (in my case, anatomical) space (in which case I know I should be using the flirt command with the -applyxfm option), which would guarantee that every map is registered to the standard space. Is that the only option I have?
Any help with this will be greatly appreciated. Sometimes it can be quite hard to get a good understanding of the details of data processing in FSL, and posting a question to this list has proved to be the most efficient way to get a definite answer.
Thanks!
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