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

[JasperVanDenBosch]

crash-20190719-183626-vandejjf-bold_transform-cde10b08-0929-4ba2-876c-386cf4bbaa0e.txt

[JasperVanDenBosch]

error originates here: https://github.com/poldracklab/niworkflows/blob/bc536192e96db5d5c02c91deaf23d1becd470f7a/niworkflows/interfaces/itk.py#L310

[JasperVanDenBosch]

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]

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

[iancharest]

Can we reallocate this dimension a posteriori?

…

On Mon, 22 Jul 2019, 18:51 Jasper J.F. van den Bosch, < ***@***.***> wrote: basically the Head Motion Correction step (bold_hmc_wf) runs off bold_reference_wf, which is generated pre-stc — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#7?email_source=notifications&email_token=AAEXT7EHGAPVJVJCR2WWXSLQAXXRFA5CNFSM4IFKLTF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2QUSPY#issuecomment-513886527>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAEXT7HH25HZ7MZRFH2RND3QAXXRFANCNFSM4IFKLTFQ> .

[JasperVanDenBosch]

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

[iancharest]

has this issue been resolved?

[JasperVanDenBosch]

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