python library: tweak execute to work with VS Code #2472

Specifically, remove the options mentioned in the log:

testing/pylint.rc:1:0: E0015: Unrecognized option found: argument-name-hint, attr-name-hint, class-attribute-name-hint, class-name-hint, const-name-hint, function-name-hint, inlinevar-name-hint, method-name-hint, module-name-hint, variable-name-hint, no-space-check (unrecognized-option)
testing/pylint.rc:1:0: R0022: Useless option value for '--disable', 'bad-whitespace' was removed from pylint, see pylint-dev/pylint#3577. (useless-option-value)

This is to address this warning:

    grep: warning: stray \ before /

Dev update

…drift_fix

population_template initialisation and drift correction fixes

…onstraints and metrics

These clash with custom memory allocators in Qt6, and haven't been
required in our builds for a long time since we no longer compile with
-march=native by default.

Besides, there's a good chance that these memory alignment issues are no
longer relevant for Eigen 3.4 - would require testing...

configure: fix Qt parameter parsing for MacOS

configure: fix Qt parameter parsing for MacOS

…mponents

This is to avoid instabilities in the estimated kurtosis values when the
estimated ADC is essentially zero, which can easily happen when
non-negativity constraints are applied.

In testing, this makes no detectable change to the estimated kurtosis
values (for those voxels with a sensible estimate), and no difference at
all to all other parameters.

…ility

…issues

…ring testing

Constrained estimation of the diffusion (kurtosis) tensor and kurtosis metrics

Dev update

Support qt6

Outlier rejection in dwi2tensor

Connected components minsize

propagate update of copyright to dev branch

Dev update

Merge of dev

Fix Qt6 deprecation warning of .pos(), .x(), and .y()

Synthstrip is a method provided in the FreeSurfer package, which is trained to operate on many different forms of brain imaging data.
This algorithm requires that either the standalone SynthStrip, or FreeSurfer version 7.3 or later, be installed on the user system.

Changed some codes based on the suggestions of Lestropie

Delete some unnecessary parts that presented in the develop period

 Modified the code, deleted the unnecessary space and variables. Edit the return section according to pylint.log

…orientation

…option

Mrview rename orientationlabel option

Various cleanups to dwi2mask synthstrip code during review of Ruobing-Chen#1.

Co-authored-by: Ruobing Chen <chrc@student.unimelb.edu.au>

Co-authored-by: Ruobing Chen <chrc@student.unimelb.edu.au>

Co-authored-by: Ruobing Chen <chrc@student.unimelb.edu.au>

 Adding the command "synthstrip-singularity, to ensure users that used the Docker or Singularity wrappers can also use this script. Adding the reference of the article that pulished the synthstrip algorithm.

…ion and description, now description and citation should appear in the command help page.

Dwi2mask synthstrip: New algorithm for dwi2mask

If the user manually provides a list of algorithms to be used, and that list does not include "b02template", do not go on to insert separate dwi2mask b02template calls for the different software algorithms that can be used within such.

…ation, CSD and bias field removal

Merge of 4313a76 and 68c532a.

Exports total global scaling multiplier that was applied for intensity normalisation.
Also includes some pylint fixes.

Resolves between #2604 and #2583.