How to Utilize Intermediate Results from fMRIPrep Without MNI Space Registration


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?

  1. Should I use tools like SPM to preprocess the raw Nifti files without transforming/warping them into MNI space?

  2. 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?

  3. 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.

While exploring the working directory, I found files stored in the following folder:

working_directory > fmriprep_24_0_wf > sub_XXXX_wf > bold_ses_01_task_rest_wf > bold_native_wf > boldref_bold > sub-XXXX_ses-01_task-rest_bold_tshift_xformresampled.nii.gz

Could this file be the one I am looking for?

I have found the following files through further exploration:

•	sub-XXXX_ses-01_task-rest_bold_tshift.nii
•	sub-XXXX_ses-01_task-rest_bold_tshift_xform.nii
•	sub-XXXX_ses-01_task-rest_bold_tshift_xformresampled.nii

I’m looking for the file that has undergone motion correction or slice time correction but has not been transformed/warped to MNI space.

I’m confused about the exact meanings of “tshift,” “xform,” and “xformresampled.”

Could someone clarify which of these files is the one I need?

Thank you very much for your help.

Hi @bcb225, and welcome to neurostars!

Why don’t you use --output-space bold which will output preprocessed images in the native BOLD space (see here: Defining standard and nonstandard spaces where data will be resampled — fmriprep version documentation)?