Describe the bug

Very similar to Issue #10, but affects (at least) both macOS and Windows
The Register* family of functions fails with an import error. The file result-3D.nii.gz is not created in the temporary directory due to an error with StringForm.

To Reproduce
Steps to reproduce the behavior:

1. Open the demo.nb file and initialize.
2. Scroll to the Registration using Elastix section and import the data.
3. Continue evaluating the code cells under Affine Transformation until you get to RegisterData which will fail with an error.

System Information :

• OS: macOS, Windows
• Mathematica version 13.0
• QMRITools Version 2.6.4

There is an "out of range" error appearing regarding StringForm which did not appear in Issue #10. This seems to be the issue and would explain why the error occurs across multiple OS.

Is your feature request related to a problem? Please describe.

It is generally best practice to avoid committing binary files such as compiled executables and zip files, as they are usually impossible to diff, add significantly to the size of the repository, and are derivable from the contents of the repository anyway. Committing binaries used to be difficult to avoid if one wished to distribute binaries for a release on GitHub.

Describe the solution you'd like

GitHub has recently enabled attaching files to releases: https://help.github.com/articles/creating-releases/. Now, when you create a release for a version tag, you can attach a zip file or any other binary data to the release on GitHub. Here is what it looks like on one of my GitHub repositories: https://github.com/rljacobson/Levenshtein/releases.

Additional context

This is only a suggestion. Feel free to disregard it if you feel it's not the right thing for your project.

This is a list of minor issues and suggestions.

• CompilebleFunctions The documentation says it "generates a list of all compilable functions." It generates a table (a list of lists wrapped in TableForm) of compilable functions, not a List. The function Compile`CompilerFunctions generates a list of compilable functions.
• SegmentMask[mask, n] It is not clear what SegmentMask is doing. The docs say, "divides a mask in n equal segments along the slice direction." What does "equal segments" mean? Equal in area? Equal in height? The plot is of a color quantized image, but the legend is continuous and in unknown units.
• For the ME-SE (TSE) T2 mapping slice profiles, in SimulateSliceEPG, the axes are not labeled.

The first one is picking nits. The second one might be my ignorance of the field of application.

Is your feature request related to a problem? Please describe.

Functions and arguments in the libarry tend to be clearly named, but documentation on the underlying implementations used are lacking. For basic manipulations/visualization functions this is not an issue as they are pretty self-explanatory, but for a number of other functions it would be helpful to specify a reference for the implementation. This can be as simple as a single paragraph summary and/or a link to a corresponding publication.

Describe the solution you'd like

It would be helpful to have the following

• A literature reference (ideally including the paper DOI) corresponding to the method implemented.
• If the implementation differs substantially from what is described, provide a brief summary of the difference and rationale behind it.

Describe alternatives you've considered

Additional context

As a concrete example from DixonTools.nb. A description provided is:
DixonReconstruct \[LongDash] Performs Dixon reconstruction of real and imaginary data.

From the name of that function, I would not know if it is performing basic two-point Dixon, IDEAL fat/water estimation or one of a number of other potential approaches based on graph-cuts, etc.? Inspection of the code reveals that it appears to be IDEAL with support for a multi-peak fat model and involves iterative potentially accounting for off-resonance and T2* decay. A potential user should be able to quickly infer what method is going to be applied without having to read the underlying source code.

Line 78 of the README has some broken markdown: "The toolbox can be loaded by using <<QMRITools". I assume it's supposed to be "The toolbox can be loaded by using <<QMRITools`"

(Part of openjournals/joss-reviews#1204)

Dear Dr. Froeling,
Recently, I am following the paper (Orton MR, Collins DJ, Koh D-M, Leach MO. Improved intravoxel incoherent motion analysis of diffusion weighted imaging by data driven Bayesian modeling. Magn. Reson. Med. 2014;71:411–20. doi: 10.1002/mrm.24649.) to do the IVIM fitting and is recommended to try your toolbox "DTITools\IVIMTools\BayesianIVIMFit2".

I followed the steps to install the toolbox then to use the toolbox. There are some problems which I have no idea to solve.

Describe the bug
The steps I tried:

1. find user directory using "FileNameJoin[{$UserBaseDirectory,` "Application"}]";
2. then copy all the files of your toolbox into the above folder;
3. new *.nb in this folder to run "<<DTITools`", then some error messages showed up:
   

Expected behavior
Since I am newcomer to Mathematica and havent find the proper solution to this problem, my purpose is to try BayesianIVIMFit2 function with 3D matrix data (xybvalue) input. I have no clues to use this toolbox, such as how to call the "BayesianIVIMFits2" function. Should I new a *.nb file and then use special or specific codes to call the function? Is there any examples to call "BayesianIVIMFits2" function to do the fitting using DWI images?
Thanks so much and waiting for your reply.

Data
The input data I wanna use is .mat with size 25625616 (xy*bvalue).

Desktop :

• [Windows 10]
• Mathematia version
• [Mathematica 11.3.0.0]

Under the "Install toolbox" heading, the README states that I need to download some external dependencies and place them in a specific folder. When I unpacked QMRITools itself those dependencies were already included, so I didn't need to download them separately.

I assume they either shouldn't be automatically included, or the instructions in the README are now unnecessary :)

(Part of openjournals/joss-reviews#1204)

The demo notebook uses SetDirectory["D:\\Werk\\Workspace\\QMRITools\\DemoData"]; - perhaps it could be SetDirectory[FileNameJoin[{NotebookDirectory[], "DemoData"}]];, which is a better default for people cloning the package via git, with a comment that says to change it if the demo data is somewhere else?

(Part of openjournals/joss-reviews#1204)

I haven't the faintest idea how testable this kind of code is, but at the very least having some basic sanity checks ("has it been installed correctly?" type checks) would be nice.

It looks like Mathematica does have a built-in testing framework: https://reference.wolfram.com/language/tutorial/UsingTheTestingFramework.html

Perhaps a "tests" notebook could be supplied along the with the "demo" notebook?

(Part of openjournals/joss-reviews#1204)

👋 🐱

Describe the bug
See attached screenshot. The labels on the buttons cannot be read.

To Reproduce
Steps to reproduce the behavior:

1. Scroll to the section DTI and IVIM
2. Evaluate all cells in the Generating diffusion gradients section.

Screenshots

Additional context
I have a 27inch high dpi iMac display.

Describe the bug
RegisterData, RegisterDataTransformSplit, RegisterDataSplit fail with an import error. It cannot find result-3D.nii.gz in the temporary directory.

To Reproduce
Steps to reproduce the behavior:

1. Open the demo.nb file and initialize.
2. Scroll to the Registration using Elastix section and import the data.
3. Continue evaluating the code cells under Affine Transformation until you get to RegisterData which will fail with an error.

Desktop (please complete the following information):

• OS: macOS
• Mathematica version 11.3

Other functions in the Register* family fail with the same error. Of course, any demonstration code depending on the output of these functions also fail.