Dear Muskaan,

combining fMRI data with so different TRs will be rather challenging, at 
least as I think you are trying to do. At least two reasons come to 
mind, one is very different tSNR across sessions which is unrelated to 
cognitive aspects (the faster you scan the lower the signal). Secondly, 
with so different TRs you are likely to be measuring very different 
signal properties across runs, and the use of the canonical HRF is open 
to discussion for short TRs (see 
https://pubmed.ncbi.nlm.nih.gov/34525404/ for a nice and recent review).

Maybe you could consider separate analyses for the different TR 
acquisitions, and rather use the results of one analyses to define 
regions or properties for the other analyses. But the interpretation 
will still be tricky, for the reasons mentioned above.

Best,

     Jorge

On 10/01/2022 08:06, Muskaan Verma wrote:
> Hello
> This is Muskaan from National Brain Research Center, India, working on my masters dissertation project.
> I am working on fMRI data, one session is resting scan with TR = 2s and another is scanned while participant was reading sentences with TR = 0.4s.
> I want to take resting scan as baseline and measure the beta (amplitude of fmri time-series) for sentence scan, then I am willing to have contrast maps with sentence>resting.
> But the issue is with the different TRs while doing first level analysis as I am unable to get design matrix in SPM. Even if I downsample the sentence scan number of volumes, it would be done by taking average over a moving window and not by eliminating volumes to resample to lower frequency.
> Please help me describing how can I do the same, how to average over the volumes or any other suitable method that can be applied.
> I would be extremely grateful.
> Thank You
> Muskaan

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