Hi all,
I'm currently working with a very atypical fMRI design and I'm having
some troubles at the initial slice timing stage in SPM. So I've got 16
runs of functional data and each run is contained in a single .nii file
(some physiological pre-processing was done in AFNI and I converted
things to .nii). The trick is that each run has a maximum number of 270
slices but many runs have far fewer slices (e.g., 100-150). I am
encountering 2 main problems dealing with this in SPM.
1/ When I go to enter the session data in the Slice Timing module, it
won't let me select a single .nii file for a session. The done button
will not let me proceed unless I select at least 2 files. Is it OK
therefore to simply have 1 session and select all 16 runs? I was under
the impression that each functional run counted as a "session" in SPM,
and so I was assuming I'd need 16 sessions in the Slice Timing module
with 1 run/session. Perhaps a solution is to convert the .nii files to
hdr/img files, as then I'd have many img files I could select for each
run. If this seems like the best solution, what's the easiest way
(preferably scriptable) to convert nii to hdr/img?
2/ How can I deal with the variable number of slices for each run? If I
put 270 (i.e., the maximum number of slices) in for the number of slices
variable, will SPM be smart enough to realize when runs are truncated
and deal with things correctly? The only problem I see with this is
that TA should technically be different for each run (since its based on
the number of TRs), and so really, I should be running 16 Slice Timing
modules each with their own Number of Slices and TA variable. I'd be
fine doing this but again, problem 1, SPM won't let me select a single
file/session...
Thanks in advance for anyone who can help.
Cheers,
Jason
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