8000 Add info on freesurfer requirement for bare install to address #1034 by neurorepro · Pull Request #1130 · nipreps/mriqc · GitHub
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Add info on freesurfer requirement for bare install to address #1034 #1130

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Sep 13, 2023
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Add info on freesurfer requirement for bare install to address #1034 #1130

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10 changes: 10 additions & 0 deletions docs/source/install.rst
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Expand Up @@ -68,6 +68,16 @@ installation should be as easy as::
After installation, make sure that all the necessary binaries are added to the ``$PATH`` environment
variable, for the user that will run ``mriqc``.

Please note that MRIQC requires Freesurfer's Synthstrip tool. If you already have Freesurfer installed,
you can get the requirements with: ::

wget https://github.com/freesurfer/freesurfer/blob/dev/mri_synthstrip/synthstrip.1.pt -P <path_to_your_freesurfer_dir>/models/

.. warning::

You will get the error `The 'model' trait of a _SynthStripInputSpec instance must be a pathlike object or string representing an existing file, but a value of '<undefined>' <class 'str'> was specified.`
if you do not install the previous Freesurfer requirement.

Otherwise, you can follow each software installation guide:
`FSL <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation>`_,
`AFNI <https://afni.nimh.nih.gov/afni/doc/howto/0>`_,
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