[DOC] Improve third-party software documentation page #1099
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@thibaultdvx @MatthieuJoulot if you have some time to take a look at this, I'd be interested to know if you think this is more clear.
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@NicolasGensollen sure! But do you expect us to follow the whole installation procedure to see if it works, or do you only want comments on the documentation? |
Just comments on whether this way of organizing things feel more clear and practical. Installing all third party software is a lot of work ! 😅 |
| @@ -19,7 +19,6 @@ You need to process your data with the [`t1-freesurfer` pipeline](../T1_FreeSurf | |||
| Do not hesitate to have a look at the paragraph **[Specifying what surface data to use](#advanced-specifying-what-surface-data-to-use)** if you want to use your own surface feature. | |||
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| ## Dependencies | |||
| <!--If you installed the docker image of Clinica, nothing is required.--> | |||
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| If you only installed the core of Clinica, this pipeline needs the installation of **Matlab** and **FreeSurfer 6.0** on your computer. | |||
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You didn't change this dependencies section like the others. Is it normal?
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Good catch ! 👍
I didn't change it on purpose because the whole page is totally outdated.
We dropped SurfStat (to use Brainstat instead which is pure Python) more than one year ago but the documentation page was never updated.
There is an issue opened to remember us to do it one day: #980
| !!! note | ||
| As for Linux, note that using the conda package should be easier in most cases. | ||
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| ### Matlab |
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Matlab is the only software that doesn't have an installation section. Is it ok?
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Good question.
It was already like this prior to this PR and I'm not sure why this is the case tbh... 🤔
I think Matlab users will have a lot of ways to install it depending on specificities which are way outside of Clinica's scope (maybe your university or institution provides some licenses and custom ways to install it for example).
I think we can keep it like this.
Partly linked to #820, this PR proposes to improve the documentation for the installation of third party softwares.
Instead of having them simply listed in a bullet point list, this PR proposes to have a proper section for each software, with subsections concerning installation steps and configuration steps.
This also changes the explanations about environment variables which were all grouped in a single section.
This could be annoying to users who might only need a subset of them.
With the proposed organization, they only need to define the environment variables described in the configuration section of the software they are interested in.
Finally, this way of organizing things makes it possible to link directly to specific software from pipeline pages instead of linking the third-party page and let the user scroll through it.
In addition, this PR proposes to add documentation about installing and configuring SPM standalone, which was missing from current doc.