Merge of PRESTUS feature updates

[jkosciessa]

Hi all,

I have merged previous changes in the DI master branch (i.e., @KTZ228's changes) and @eleonoracarpino's open pull request into my recent version.

This includes small feature updates:

• calculation and plotting of CEM43 heating values (@sirmrmarty)
• required external tools (e.g., kWave) are included as submodules; this may have consequences for binary downloads (?)

I have also merged @eleonoracarpino's pseudoCT branch. Despite rebasing that branch, this turned out messier than I hoped, so I had to manually redo some recent changes.

I am currently testing this full merge, and will also try out the pseudoCT implementation. If I run into hiccups, I will update this pull request.

It would be great if someone else can also validate this version prior to a merge.

[jkosciessa]

Commit f14f5e0 integrated the three parts of the pseudoCT code into a continuous function with relative paths etc.

Successfully ran this with a Donders 2deg UTE image. All fixed parameters, so no dependencies (beyond software toolboxes). Added an example call script as part of the documentation.

[mekman]

@jkosciessa do you agree that I can add the .Rhistory to .gitignore bc we don't need it, right?

[jkosciessa]

Yes, but let's first delete it, otherwise it will remain in the repo forever. Taking care of it now.

[jkosciessa]

3195d93 is a big one.

As specified in the commit:

This commit integrated smooth_and crop.m and setup_medium.m across setup variants to harmonise how tissues are labeled. All previously hardcoded tissue labels are now referring to the config. The medium mask output of pseudo-CT generation has been reindexed according to the default layered setup and the conversion to tissue mask labels is performed in smooth_and_crop.m similar to the original layered setup. Minor documentation additions. Function getidx.m has been added to rapidly grab tissue labels from the parameters structure.

I forgot a few things in there:

• Now all figures up to simulation onset should be consistently saved via saveas with individual figure handles. This should avoid any saved figures with grey background.
• In addition to pseudoCT, smooth_and crop.m now also handles the scenario of a skull-only setup, removing the need for an independent function.

I do not expect any backcompat issues, but given that changes relate to the tissue mapping, it would be good to inspect the outputs in the debug folder that will be created when running the pipeline, in particular checking the coherences ofsound_speed.nii.gz and density.nii.gz with the specified values.

I am currently running both layered and layered+pCT variants. Up to simulation onset, the medium properties looks correct. Acoustic and heating outputs are also in expected ranges.