Fmriprep 1.0.6-2 issues: semi-random brain mask failure and super bright areas in epi

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It happened, 1.0.7 is out!

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Fantastic! Will test and report back!

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All worked fine now (tested the originally problematic subject, another lesion brain and some normal brains).
Sorry for the slow response!

Thanks for getting at this so quickly!

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Dear fMRIprep experts:

I’m currently preprocessing data with frmiprep and would like to ignore both: fieldmaps and slicetiming. To do that I’ve specified, as suggested in this thread, --ignore fieldmaps slicetiming.

I’m running fmriprep-v20.2.0 via singularity.

When I do that I get the following error:

fmriprep: error: argument --ignore: invalid choice: ' ' (choose from 'fieldmaps', 'slicetiming', 'sbref', 't2w', 'flair')
./run_fmriprep_seb_noST.sh: line 23: --use-syn-sdc: command not found

I’ve tried most other conceivable permutations of adding both, i.e. --ignore fieldmaps, slicetiming, --ignore [fieldmaps slicetiming] etc and also adding ignore twice.

Could you help me with this issue?

Thanks,

Sebastian