fMRIprep - T2w outputs

1

Hi,

We provide T1w and T2w data in anat folder(In the following way) to run fMRIprep.
sub-50018_ses-1_T1w.json
sub-50018_ses-1_T1w.nii.gz
sub-50018_ses-1_T2w.json
sub-50018_ses-1_T2w.nii.gz

After running fMRIprep I only see T1w outputs like following?

sub-50018_desc-preproc_T1w.nii.gz
sub-50018_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
sub-50018_from-T1w_to-fsnative_mode-image_xfm.txt
sub-50018_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
sub-50018_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz

How can get T2w outputs like these T1w outputs? What are the options I should use to get those?

Thank you
Best,
Sameera

2

Hi Sameera,

We don’t currently generate any modified T2w images, but registering T2w images to the T1w template is an open issue: https://github.com/poldracklab/smriprep/issues/69

Please feel free to comment there on what you’re looking for in your outputs.

Best,
Chris

3

Thank you @effigies . Sure I will comment on that issue.