New warning about affines pops up after updating to fMRIprep 1.0.0-rc10 from rc8?

fmriprep

#1

Hello,

I tried re-running the new version of fMRIPREP (1.0.0-rc10) on a subject that I had previously processed successfully with no warnings or issues using fMRIPREP 1.0.0-rc8. With this new version, I have this new warning that starts spamming hundreds of times and did not appear in rc8:

171110-02:11:12,311 interface WARNING:
	 Affines of input and reference images do not match, CopyXForm will probably make the input image useless.

Any idea of what it may be? Is the warning harmless? Should I go back to rc8? I’m including below the beginning of the log file, if it helps.

Thank you!

Running fMRIPREP version 1.0.0-rc10:

  • Participant list: [‘226854’].
  • Run identifier: 20171110-020751_ed44371c-0885-4483-9b74-390d9e535bcd.

171110-02:07:53,825 workflow WARNING:
No fieldmaps found or they were ignored, building base workflow for dataset /data/h_zald_lab/Fran/tts_test/BIDS_TTS_Test/sub-226854/func/sub-226854_task-mid_run-01_bold.nii.gz.
171110-02:07:57,92 workflow WARNING:
No fieldmaps found or they were ignored, building base workflow for dataset /data/h_zald_lab/Fran/tts_test/BIDS_TTS_Test/sub-226854/func/sub-226854_task-mid_run-02_bold.nii.gz.
171110-02:08:00,980 workflow WARNING:
No fieldmaps found or they were ignored, building base workflow for dataset /data/h_zald_lab/Fran/tts_test/BIDS_TTS_Test/sub-226854/func/sub-226854_task-mid_run-03_bold.nii.gz.
171110-02:08:13,497 interface WARNING:
No ‘t2w’ images found for sub-
171110-02:08:13,497 interface WARNING:
No ‘fmap’ images found for sub-
171110-02:08:13,498 interface WARNING:
No ‘sbref’ images found for sub-
171110-02:09:43,908 cli WARNING:
Captured warning (<class ‘UserWarning’>): The behaviour of affine_transform with a one-dimensional array supplied for the matrix parameter has changed in scipy 0.18.0.
171110-02:10:05,844 niworkflows INFO:
Successfully created report (/data/h_zald_lab/Fran/tts_test/work_226854_nofs/fmriprep_wf/single_subject_226854_wf/func_preproc_task_mid_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/mask_reportlet/report.html)
171110-02:11:12,311 interface WARNING:
Affines of input and reference images do not match, CopyXForm will probably make the input image useless.
171110-02:11:12,313 interface WARNING:
Affines of input and reference images do not match, CopyXForm will probably make the input image useless.
171110-02:11:12,341 interface WARNING:
Affines of input and reference images do not match, CopyXForm will probably make the input image useless.
171110-02:11:12,349 interface WARNING:
Affines of input and reference images do not match, CopyXForm will probably make the input image useless.
171110-02:11:12,400 interface WARNING:
Affines of input and reference images do not match, CopyXForm will probably make the input image useless.


#2

Hi @yeehaw. I would check your outputs to be sure, but it should be harmless. We’ve recently made changes that make the warning more likely to occur, but less likely than ever to indicate anything is actually amiss.

If there is an actual problem, it will most likely appear in the reports as contours that don’t align with the images they overlay, or possibly a “pulsing” image where the before and after images are very clearly misaligned. If you do see real issues, please open an issue on Github.