Best Practices for Removing Dummy Scans After fMRIPrep Before Tedana Processing

[tsalo]

@AJavan

3. Apply the transformations provided by fMRIPrep to co-register the images to MNI space (Native → T1 → MNI). The transformations are the ones estimated from the non-trimmed images.

4. Resample the image from 3mm to 2mm isotropic.

I wouldn’t do these two steps. Instead, it is probably better to (1) remove the dummy volumes from the echo-wise files, (2) run tedana on those trimmed files, (3) remove the dummy volumes from the MNI-space optimally combined file from fMRIPrep, and (4) use the tedana ICA components to denoise the trimmed MNI-space file. That way, you don’t have to worry about doing any resampling or warping.

@AJavan

However, the anat directory in the fMRIPrep output contains only the transformation file:
“sub-MTL0002_ses-FU84_acq-MPRAGE_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5”, and not a separate transformation for MNI152NLin2009cAsym:res-2.

The transform doesn’t specify the resolution. You would apply the transform and use a reference image in the target resolution to get your data in the desired space and resolution.