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Handle missing magnitude2.nii(.gz) files #709

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effigies opened this Issue Sep 18, 2017 · 2 comments

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effigies commented Sep 18, 2017

See https://neurostars.org/t/fmriprep-fieldmap-phasediff-error-file-magnitude2-not-found/712

If we can support distortion correction without magnitude2.nii, we should. If it's the case that we might get magnitude1.nii files with two volumes, we should handle that case, as well. And if we don't have enough data to perform distortion correction, we should note that in the summary and not crash.

@oesteban oesteban self-assigned this Oct 9, 2017

@oesteban oesteban added this to the Phase II milestone Oct 20, 2017

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chrisfilo commented Oct 26, 2017

There is one more report on NeuroStars https://neurostars.org/t/fmriprep-field-mapping-data/755/5

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roniiw commented Oct 26, 2017

I have encountered the same issue,
I tried duplicating the magnitude file as suggested here- https://neurostars.org/t/fmriprep-fieldmap-phasediff-error-file-magnitude2-not-found/712/3, but that didn't work.

The output of nib-ls is - int16 [106, 106, 33, 2] 2.00x2.00x4.80x0.40 sform

I'm also attaching the error log
59f1dfe38b4b240001c5a661.txt

oesteban added a commit to oesteban/fmriprep that referenced this issue Oct 26, 2017

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