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dwiintensitynorm: Fix bug introduced in #1389#1534

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Lestropie merged 2 commits intodevfrom
dwiintensitynorm_fix
Jan 14, 2019
Merged

dwiintensitynorm: Fix bug introduced in #1389#1534
Lestropie merged 2 commits intodevfrom
dwiintensitynorm_fix

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Function app.mrconvertOutputOption() can only be applied when run.command() is calling mrconvert; the command-line options it exploits are not present in other binaries.

Function app.mrconvertOutputOption() can only be applied when run.command() is calling mrconvert; the command-line options it exploits are not present in other binaries.
@Lestropie Lestropie merged commit ca806b0 into dev Jan 14, 2019
@Lestropie Lestropie deleted the dwiintensitynorm_fix branch January 14, 2019 02:12
Lestropie added a commit that referenced this pull request Jan 31, 2019
- dwipreproc:
  - Make use of command example usage functionality to demonstrate usage of four -rpe_* options.
  - Give more thorough description of -align_seepi option, and update some description text that was written prior the the existence of that option.
  - Erase the commented text at the head of the file, which formed a pragmatic 'help page' way back before creation of the MRtrix3 Python API.
  - If CUDA eddy fails, write its output to a text file in the scratch directory nonetheless.
  - Print outputs from topup and eddy for -info verbosity and above, but additionally provide --verbose command-line options to these commands if running script at -debug level.
- foreach:
  - Break up string substitutions across individual description paragraphs.
  - Use example usage functionality to demonstrate basic command-line usage of command without triggering a sphinx warning.
  - Also add second example usage to demonstrate multi-threading.
- dwinormalise group:
  - Add description paragraph describing necessity to use .mif format DWI files as gradient tables must be embedded (echoes #1414).
  - Propagate bug fix #1534.
- mrtrix3.path: Provide quote() function for placing quotation marks around filesystem path if necessary as part of a command string.
- dwi2response: For msmt_5tt and dhollander algorithms, use path.quote() to support use cases where the scratch directory location contains whitespace.
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