Dockerfile building from a PyTorch base image to facilitate running FastSurfer (GPU). Testing this image for FastSurfer - once built as smriprep:fastsurfer_dev - can be performed with the following command:

docker run --gpus all --entrypoint /bin/bash -v /path/to/bids:/data -v /path/to/bids/derivatives/fastsurfer:/output -v /path/to/freesurfer/license:/fs60/license --rm --user `id -u` smriprep:fastsurfer_dev /opt/FastSurfer/run_fastsurfer.sh --fs_license /fs60/license --t1 /data/sourcedata/sub-SUBJECT/ses-SESSION/anat/sub-SUBJECT_ses-SESSION_T1w.nii.gz --sid sub-SUBJECT --sd /output

Checks FreeSurfer subjects dir for presence of files in mri/ with names indicating processing with FastSurfer, and returns a boolean fastsurfer_bool to indicate that FastSurfer is being used instead of Freesurfer. For development purposes, this also touches files that are expected outputs of Freesurfer, but not produced by default in FastSurfer. (Addresses nipreps#278 & Deep-MI/FastSurfer#21)

Add logger for the check_fastsurfer function to indicate if evidence of FastSurfer surface recon was used to generate the given subjects_dir

Adds the check_fastsurfer function call to log FastSurfer outputs detected in subjects_dir and touch mri/aseg.auto_noCCseg.label_intensities.txt to prevent failure in surfaces.py as a temporary fix for nipreps#278

Removes currently unused fastsurfer_bool variable

Adds FastSurfer argument to support FastSurfer as a surface processing option (nipreps#278)

Add citations for FastSurfer: 1mm isotropic original paper = fastsurfer, 2022 hires version (NOT YET IMPLEMENTED) = fastsurfer_hires

Adds python wrapper for FastSurfer (nipreps#278)

Adds affiliation to contributors for work regarding nipreps#278

Fix typo

Add researcher type

Address PEP8 blankspaces flag

Address PEP8

Address PEP8

Fix fail to build docs in CircleCI observed in testing draft changes made to PR nipreps#280. 

```
#!/bin/bash -eo pipefail
make -C docs SPHINXOPTS="-W" BUILDDIR="_build/no_version_html" html

make: Entering directory '/tmp/gh-pages/docs'
PYTHONPATH=/tmp/gh-pages sphinx-build -b html -d _build/no_version_html/doctrees  -W . _build/no_version_html/html
Traceback (most recent call last):
  File "/home/circleci/.local/bin/sphinx-build", line 5, in <module>
    from sphinx.cmd.build import main
  File "/home/circleci/.local/lib/python3.8/site-packages/sphinx/cmd/build.py", line 23, in <module>
    from sphinx.application import Sphinx
  File "/home/circleci/.local/lib/python3.8/site-packages/sphinx/application.py", line 42, in <module>
    from sphinx.highlighting import lexer_classes, lexers
  File "/home/circleci/.local/lib/python3.8/site-packages/sphinx/highlighting.py", line 30, in <module>
    from sphinx.ext import doctest
  File "/home/circleci/.local/lib/python3.8/site-packages/sphinx/ext/doctest.py", line 28, in <module>
    from sphinx.builders import Builder
  File "/home/circleci/.local/lib/python3.8/site-packages/sphinx/builders/__init__.py", line 24, in <module>
    from sphinx.io import read_doc
  File "/home/circleci/.local/lib/python3.8/site-packages/sphinx/io.py", line 42, in <module>
    from sphinx.util.rst import append_epilog, docinfo_re, prepend_prolog
  File "/home/circleci/.local/lib/python3.8/site-packages/sphinx/util/rst.py", line 22, in <module>
    from jinja2 import environmentfilter
ImportError: cannot import name 'environmentfilter' from 'jinja2' (/home/circleci/.local/lib/python3.8/site-packages/jinja2/__init__.py)
make: *** [Makefile:61: html] Error 1
make: Leaving directory '/tmp/gh-pages/docs'

Exited with code exit status 2

CircleCI received exit code 2

```
From suggested fix for similar behavior: mkdocs/mkdocs#2799

Fix docstring list end without a blank line error

Update example of commandline FastSurfer usage to docstring, formatting of input spec docstring

Adds FastSurfer recon workflow per discussion in nipreps#280

Removes unwanted blank line before `elif`

Fixes memory requirement for FastSurfer recon

Removes `/download` at the end of Convert3D URL to debug error in curl output and CircleCI build image test

Debug build_docs error 

> Warning, treated as error:
> /tmp/gh-pages/smriprep/interfaces/fastsurfer.py:docstring of smriprep.interfaces.fastsurfer.FastSCommand:44:Definition list ends without a blank line; unexpected unindent`

ENH: Add FastSurfer workflow support (WIP)

Install `locales` before installing convert3d

Replace erroneous `.` with `,`

Changes from pytorch image based on Ubuntu 16.04 to Ubuntu 20.04 base image modified from the dev branch of FastSurfer (https://github.com/Deep-MI/FastSurfer/blob/0749f38e656ed0da977c408b4383db88e1a8b563/Docker/Dockerfile) to resolve ca-certificates errors in build

Adds parameters and workflows for FastSurfer to base wf

Returns FreeSurfer style outputs if FastSurfer is enabled

…to_native_wf