afni.nimh.nih.gov

Hi PT,

Thank you so much for your reply. Yes,the FMRIprep command above should be outputting the EPIs in alignment with the subject anatomical , basically in a "native" subject space).

And the A and B outputs are:
A:

N-1 header file 'sub-1_task-checker_acq-TR156_space-T1w_desc-brain_mask.nii.gz', num_fields = 2
  name                offset  nvals  values
  ------------------- ------  -----  ------
  qform_code           252      1    2
  sform_code           254      1    2

B:

N-1 header file 'sub-1_desc-preproc_T1w.nii.gz', num_fields = 2
  name                offset  nvals  values
  ------------------- ------  -----  ------
  qform_code           252      1    1
  sform_code           254      1    1

Many thanks for your help!

---Aaron