Module bold_std_trans_wf has no output called poutputnode.bold_aseg_std

[shaohanyu2017]

Dear fmriprep experts,
When I am trying to run the latest version fmriprep (1.4.0) with the --output-space fsnative, I received the following error. How I can solve the issue? With many thanks!

Exception: Some connections were not found
Module bold_std_trans_wf has no output called poutputnode.bold_aseg_std

Module bold_std_trans_wf has no output called poutputnode.bold_aparc_std

Module bold_std_trans_wf has no output called outputnode.bold_aseg_std

Module bold_std_trans_wf has no output called outputnode.bold_aparc_std

[lukassnoek]

I had the same error, which I think is caused by the init_bold_std_trans_wf function:

freesurfer = [k for k in standard_spaces.keys()
                  if k.startswith('fs') and k != 'fsLR']

which later adds the bold_aseg/aparc_std nodes based on this freesurfer variable:

if freesurfer:
        output_names += ['bold_aseg_std', 'bold_aparc_std']

It turns out that standard_spaces only includes spaces that are not part of the "non-standard references":

NONSTANDARD_REFERENCES = ['anat', 'T1w', 'run', 'func', 'sbref', 'fsnative']

So, when you don't add some kind of "fsaverage*" output to your --output-spaces argument, fmriprep will crash. So, to circumvent this issue, I added fsaverage to my --output-spaces. Ideally, however, I'd like to get the aseg/aparc segmentations/parcellations also without specifying any freesurfer-based output space (e.g., only T1w).

Would this be possible?

[oesteban]

So, when you don't add some kind of "fsaverage*" output to your --output-spaces argument, fmriprep will crash. So, to circumvent this issue, I added fsaverage to my --output-spaces. Ideally, however, I'd like to get the aseg/aparc segmentations/parcellations also without specifying any freesurfer-based output space (e.g., only T1w).

Would this be possible?

Sure, what you are describing is very related to #1631. Please feel free to reopen that issue and elaborate there on how you would like to see this implemented.

For now, I'll address this error independently of such conversation to avoid crashing for this reason.