add literature references for the methods used about qmritools HOT 11 CLOSED

Hi indeed that is lacking but can easily be added.

I like you suggestion to add paragraphs to the guide pages of the documentation with links to the DOI of the manuscripts (since i like my function help to be as clear as possible).

I will only do this for the main processing functions scuh as T2 fitting dixon reconstruction denoising etc. that have a solid basis in literature.

I will let you know when they are updated.

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@grlee77 do you find this sufficient?

In case of dixon reconstruction and other more complicated fitting functions i try to be clear in the help of each function.

I'll try to go through all the functions and guides to see if i can make anything more clear but this probably will take a while.

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Yes, just having those DOI links would already a huge improvement. I saw that you had many of these references in the manuscript itself, but it is more useful to the user to have them easily found in the docs.

The parameter help as shown above for Dixon looks good to me, although it wouldn't hurt to add the units expected for the parameters when applicable (e.g. ppm for DixonFrequencies) ,

It would also be useful to specify in the DixonReconstruct descriptions whether it supports both 2D and/or 3D data for the inputs.

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A couple of other random things I noticed when looking over the code:

1.) PhysioTools: What format(s) of physiology log files is this supposed to process? I think each vendor uses their own format for respiratory, ECG and/or PPU logs.

2.) I saw the term "Overplus" in relation to diffusion gradients. Isn't this a Philips-specific term to refer to gradients played out along a combination of the X/Y/Z axes to allow shorter echo times at a given b-value? I'm not sure users coming from other systems would know what that is referring to.

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@grlee77 i have added around 20 dois troughout the guides in the documentations, it is currently compiling and will upload it once it is done. for completeness i have also generated a PDF of the function documentation such that is readable outside mathematica.
https://github.com/mfroeling/QMRITools/blob/master/QMRITools/All-Functions.pdf
With the new paper i tried to make clear what is and what is not in the demo file, since some tools such as the physlogging i hardly ever use my self.

indeed adding what input (1D, 2D, 3D or 4D) for each function and what units would make some more clear. However the full documentation is allmost 100 pages so i have to see if i can find the time (and willingness) to go through all and figure out where such additions are needed.

1. yes every vendor uses their own format for phys logging. Im not even sure if the current fucntion stille works on the latest philips log. I havent used the functionality in a while.
2. indeed overpuls is a term i adopted from the philips platform, and is used in generateGradient(GUI) not sure how else to call or explain this, but the visual representation of the gradients show what it is.

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Thanks for adding the DOIs. Having a PDF is nice for reference outside of Mathematica. I don't know if exporting to HTML is similarly easy, but hosting the docs somewhere that they get indexed by Google, etc., might help potential users find your software.

As far as adding dimensions/units, perhaps just start with a few of the main functions likely to be of interest to end users such as Dixon, T2 fitting and DTI? (I am not saying you HAVE to do this for purposes of the review, it is just a suggestion to improve usability).

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@grlee77 will defininatly add this for the main functions. Yes i can generate an html for the documentation using the mathematica workbench, and will see if it is possible to host this online with the repository.

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I see the DOIs were added to various files in your recent commit to master, but I do not see them in the PDF you linked above. Was that built prior to adding them or am I missing something?

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@grlee, indeed i have updated the guide pages which are not included in the PDF. im working on the function files this week including the units where apropirate and also including the DOI on a function level.

once done i well recompile the help and regenerate the PDF which then should include the DOIs.

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@grlee the DOI numbers are now also included in the code as well as in the documentation and PDF file.
https://github.com/mfroeling/QMRITools/releases/download/2.0/All-Functions.pdf

I still have to do a recompile of the reference page database and will see if the HTML build works.
Adding units to the help files is next on my list.

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@grlee i have created a new release that also includ a html version of the documentation, I have also added all DOIs and units of the parameters where apropriate.

https://github.com/mfroeling/QMRITools/releases/tag/2.1

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