Preprocess BOLD in subject's anat space, but compute transformation to MNI space

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Hello,

I’m preprocessing an fMRI dataset with fMRIPrep v23.0.2. I would like to preprocess the BOLD scans in the participants’ anat space, because I have manually segmented ROIs of the medial temporal lobe, and want to avoid warping the data. For this, I will use the --output-spaces anat flag in the fMRIPrep command.

However, I may have to use some additional ROIs from atlases in MNI space. For this, I would need each participant’s T1w-to-MNI transformation so that I can back-transform the ROIs from MNI space to the participant’s T1 space. Is there a way to get preprocessed BOLD in the anat space, but also instruct fMRIPrep to compute and save the T1w-to-MNI transformation in one go?

Thank you!
Mrinmayi

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fMRIPrep should produce a T1w-to-MNI152NLin6Asym transform automatically, even if you don’t request MNI-space outputs with --output-spaces.

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