Adding FreeSurfer commands (for validation tests)

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Description

This PR includes a few additional commands and binaries in the pruned Freesurfer install that are used in the FastSurfer validation pipeline.

The validation pipeline is being modified to run FastSurfer processing and Freesurfer commands through the FastSurfer Docker image. Therefore, the following Freesurfer binaries/scripts and their required files have been included:

• asegstats2table
• aparcstats2table
• mris_preproc
• mri_glmfit

This increases the FastSurfer Docker image size by ~60MB.

Note:

• The stats Python scripts necessitate the inclusion of Freesurfer's packaged Python interpreter and some libs to work. These account for nearly all of the size increase (> 57MB).
• The Dockerfile was changed to not delete/overwrite Freesurfer's Python.

Secondary Dependencies

This section lists the binaries, scripts, and files that are needed by the aforementioned Freesurfer binaries/scripts.

asegstats2table and aparcstats2table

Python packages:

• fsbindings

mris_preproc

Binaries:

• fname2stem
• fspython
• mri_surf2surf

Scripts (without the following, the script still runs through but with silent failures that lead to incorrect results):

• isanalyze
• isnifti

mri_glmfit

None.

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UPDATE

The Freesurfer Python interpreter and other extra files were removed; only the stats scripts' non-native dependency fsbindings.legacy is now included in the Freesurfer Python files.

For this to work, the fsbindings __init__.py is edited in install_fs_pruned.sh to make the submodule accessible without needing the pre-compiled library (.so file), which would have required Freesurfer's Python version to run.

The following is an example command for running asegstats2table using a pre-built FastSurfer Docker image:

docker run --gpus=all --rm --name fastsurfer_asegstats \
	-v ${freesurfer_dir}:/freesurfer_dir -v ${subject_list_dir}:/subject_list_dir \
	-v ${subjects_dir}:/subjects_dir -v ${output_dir}:/output_dir 
	-e FS_LICENSE="/freesurfer_dir/.license" -e SUBJECTS_DIR="/subjects_dir" --entrypoint asegstats2table \
	--user $(id -u):$(id -g) fastsurfer:gpu \
	--subjectsfile=/subject_lists_dir/${subject_list_file} --meas=volume \
	--tablefile=/output_dir/aseg.${run_id}.volume.txt --delimiter=space --stats=aseg.stats

This modification reduces the additional image size from ~60MB to ~40MB.

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EDIT: Removed an incorrect comment that "the asegstats2table and aparcstats2table commands (shell scripts) can not be used directly, because they explicitly call the Python scripts using Freesurfer's Python interpreter. Instead, the user must run the Python scripts. "