Hello,
I am seeking guidance on how to utilize intermediate results from fMRIPrep. I started with raw Nifti files (unprocessed) and used fMRIPrep for preprocessing, which ultimately provided files transformed/warped into MNI space.
However, I am interested in obtaining results from the preprocessing steps that do not include registration to MNI space. For example, I need results that have undergone motion correction or slice time correction but have not been further transformed/warped into MNI space.
I noticed that the fMRIPrep working directory contains various files such as nii.gz and xfm.txt. How can I obtain the results from the preprocessing stage before the MNI space registration?
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Should I use tools like SPM to preprocess the raw Nifti files without transforming/warping them into MNI space?
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Should I locate the xfm.txt or nii.gz files from the fMRIPrep working directory that pertain to the stage right before MNI space registration and perform inverse matrix operations?
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Alternatively, should I find all transformation matrix (xfm.txt) files in the fMRIPrep working directory that were applied from the raw files to the final outputs and apply these to the raw files?
I would appreciate any assistance.
Thank you.