I have searched the archives and tried a few things I read there, but I am not having much luck. This feels like a very basic question, but I can't seem to get it working the way I need. I apologize if this is a repeat post, but I was not able to find a solution that works for me.
What I am trying to do: I am trying to register a functional scan to the MNI atlas. I have successfully done this with flirt (turning off all smoothing, etc because I only want the transform step), but my output file is a single frame (reference file?). I have tried to do this with applyxfm as well, but the image gets moved around and at least one view ends up chopped off (I'm guessing because the voxel size of the acquired image isn't the same as the atlas?).
It's frustrating because this feels like it should be a rather simple function, but I can't seem to find anything about how to do this transform without running it through all the steps of FEAT. I'm hoping someone can point me in the right direction or to the proper tool (or perhaps knows what I'm doing wrong with FLIRT if that is, indeed, the correct tool to use).
Thanks in advance!
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