Changes necessary for upcoming copyright notice changes to work.

Script ensures conformity of copyright information in source file headers.

Warning regarding comparison between signed and unsigned integers on some compilers under Eigen 3.2.

Math::Zstatistic: Fix compiler warning

Copyright

Empty string output by Path::dirmane() if the location of the list file is the current working directory would lead to an erroneous Exception being thrown, as that string being empty is also used as a flag to indicate that none of the candidate directories were reliable references for finding all subject files.
This fix uses "." rather than "" for the current working directory, so that if a valid Exception is indeed thrown the error message should make more sense.

CohortDataImport::initialise(): Fix for cwd

Add .gitattributes file

Caused mrtransform to fail when the number of se_epi images made it interpretable as SH coefficients (e.g. 6)

dwifslpreproc: add missing reorient_fod option

progressbar: fix behaviour under redirection

Due to copying header properties from the original input DWI in order to preserve header key-values and appropriately concatenate "command_history", the contents of "dw_scheme" were being erroneously overwritten by the original gradient table of the input DWI. This fix ensures that the updated version generated during the script - whether including motion correction and/or explicit volume recombination - is propagated to the final output image.

- Remove redundant control of scalar-based thresholding UI controls.
- Fix off-by-one error between streamline vertices and scalar / colour by endpoints data.
- Fix erroneous assert() call when loading track scalar file for the purpose of thresholding.
- Fix scaling rate of lower / upper threshold by scalar file AdjustButtons.

dwifslpreproc: Don't discard modified dw_scheme

For some reason, sphinx doesn't handle <sup></sup> properly.

Due to libtiff already being installed with a different version than
latest. See this link for details:
Homebrew/brew#2491 (comment)

Docs: DW handling: Describe shells

Pylint fixes for master

Fixes case where there is no phase encoding contrast present in the SE_EPI images (and hence they need to be combined with the DWI b=0 data for tuopup to possibly be applicable), and also the SE-EPI volumes are defined on a different image grid to the DWIs.

dwifslpreproc: Fix for rare usage

dwidenoise: limit patch size to image dimensions

dwifslpreproc: fix help for -align_seepi option

- afdconnectivity: Add reference and hyperlink to documentation page.
- tcksift2: Add reference for use of -linear option.
- mrtransform: Fix typo in -reorient_fod help text.

Minor command docs updates

Prevents unhandled Python exception from attempting to access number of volumes in a 3D image.

dwifslpreproc: On -rpe_pair, ensure -se_epi is 4D

This fixes #2245

Fixes issue when double-clicking quarantined files on macos.

Since these currently cause CI to fail

This step takes a long time, is prone to failure, and unnecessary at the
moment - we can rely on the default install being sufficiently up to
date.

This simply clamps values of the input data at zero before taking their
mean per-shell, which seems to fix issues raised in #2248.

Update copyright notice

…_data

dwi2response dhollander: fix handling of data with negative values