Charestlab/pyslicetime

Number of transforms (1035) found in the ITK file does not match the number of input image files (1863)

Opened this issue · 7 comments

JasperVanDenBosch commented

here is the high-level problem:

https://github.com/poldracklab/fmriprep/blob/master/fmriprep/workflows/bold/base.py#L601


    workflow.connect([
        # Generate early reference
        (inputnode, bold_reference_wf, [('bold_file', 'inputnode.bold_file')]),
        # BOLD buffer has slice-time corrected if it was run, original otherwise
        (boldbuffer, bold_split, [('bold_file', 'in_file')]),
        # HMC
        (bold_reference_wf, bold_hmc_wf, [
            ('outputnode.raw_ref_image', 'inputnode.raw_ref_image'),
            ('outputnode.bold_file', 'inputnode.bold_file')]),
JasperVanDenBosch commented

basically the Head Motion Correction step (bold_hmc_wf) runs off bold_reference_wf, which is generated pre-stc

iancharest commented
JasperVanDenBosch commented

I'm thinking we could perhaps connect boldbuffer to bold_hmc_wf..

iancharest commented

has this issue been resolved?

JasperVanDenBosch commented

Not as far as I know. We have to somehow adapt the metadata afterwards but I'm not sure where.