Thanks for the reply Taylor,
In the html report, the figure all point to figure labels with ‘echo-1’. For example, sub-018/figures/sub-018_ses-001_task-faces_echo-1_rois.svg
Moreover in my working directory I only find the following files:
about func_preproc_ses_001_task_faces_echo_1_wf
anat_preproc_wf func_preproc_ses_001_task_rest_echo_1_wf
bids_info func_preproc_ses_002_task_faces_echo_1_wf
bidssrc func_preproc_ses_002_task_rest_echo_1_wf
ds_report_about summary
ds_report_summary
Does this indicate that only echo_1 is analysed?
However, when I go to the output directory the files are not labeled with ‘echo…’. For example, fmriprep/sub-018/ses-001/func/sub-018_ses-001_task-faces_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
Does this mean that the html report and working file label is indicating the echo-1 is being used as some reference, but actually the correct, optimally combined, images can be found in the output folder?
ie., the following image is the optimally combined image: sub-018_ses-001_task-faces_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
I will examine your code and try to omit --force-syn.
Kind regards,
Gershon.