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If an input image to dwicat is a 3D image containing a single b=0 volume, it should be possible to continue processing; but it is necessary to validate such, and to bypass the dwiextract step.
For the manual response function estimation, a brain mask is not needed or supported. However, currently, a brain mask is always calculated if one is not provided. This is unnecessary and can also lead to crashes whenever dwi2mask fails (e.g. exotic data, simulations, ... exactly the use-cases where you would use manual response estimation).
…it supports a mask
dwicat: Support 3D images
As discussed on the forum: https://community.mrtrix.org/t/dwifslpreproc-error-somewhere-after-the-topup-process/5248/4 This is to avoid potential mismatch with the original DWI series in the subsequent mrcat call, which can result in the DW scheme being labelled as 'variable' and removed altogether.
add .nojekyll file to documentation update script
…dw_scheme dwifslpreproc: strip DW encoding from padding slice
dwi2response manual: avoid checking and calculating a brain mask
README.md: Add Twitter reference
Documentation (Fixels and Dixels): double negative typo
This disables a lot of changes to allow compatibility with Python 2. These will be re-enabled on dev with a view to dropping Python 2 support in future releases.
Based on feedback in #2398.
minimal set of changes to pass pylint 2.11.1 tests
As mentioned in #2402, replace dead link with one to relevant wiki page on community forum
Fix link to advanced debugging help page
CONTRIBUTING.md: Revise text RE: target branch for docs changes
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Regular merge of
masterintodev, this time to deal with the changes made to deal with the manypylint2.11.1 warnings.One point worth mentioning is that I've left
consider-using-f-stringdisabled, since these were introduced in Python 3.6. As far as I can tell, we can't use them without breaking compatibility with Python 3.5 or earlier. We are dropping support for Python 2, but I'm not sure we should immediately require Python 3.6+. Open for discussion...