[Module][WIP] fslfirst

[PaulBautin]

Describe your changes

This module adds a segmentation tool to perform subcortical structure segmentation using FSL FIRST.

run_first_all is no more part of the containers_scilus_1.6.0.sif . Error when testing: .command.sh: line 2: run_first_all: command not found

Is there another container to use for full FSL toolbox?

Say which test data are used by your module

${params.test_data_base}/heavy/anat/anat_image.nii.gz

Checklist before requesting a review

• Create the tool:
  • Edit ./modules/nf-scil/<category>/<tool>/main.nf
  • Edit ./modules/nf-scil/<category>/<tool>/meta.yml
• Generate the tests:
  • Edit ./tests/modules/nf-scil/<category>/<tool>/main.nf
  • Edit ./tests/modules/nf-scil/<category>/<tool>/nextflow.config
  • Add test data locally for tests with the fork repository
  • Generate the test infrastructure and md5sum for all outputs
• Ensure the syntax is correct :
  • Check indentation abides with the rest of the library (don't hesitate to correct others !)
  • Lint everything. Ensure your variables have good names.

[PaulBautin]

It seems that run_first command is not found in the scilpy containers i have tested -- this probably explains the error: Missing output file(s) *_all_fast_firstseg.nii.gz. when testing the module

These are the commands that do not work in test.com:

/usr/share/fsl/5.0/bin/run_first -i anat_image -t anat_image_to_std_sub.mat -n 50 -o test-L_Accu_first -m /usr/share/fsl/5.0/data/first/models_336_bin/L_Accu_bin.bmv; /usr/share/fsl/5.0/bin/first_boundary_corr -s test-L_Accu_first -o test-L_Accu_corr -i anat_image -b fast
/usr/share/fsl/5.0/bin/run_first -i anat_image -t anat_image_to_std_sub.mat -n 50 -o test-L_Amyg_first -m /usr/share/fsl/5.0/data/first/models_336_bin/intref_thal/L_Amyg.bmv -intref /usr/share/fsl/5.0/data/first/models_336_bin/05mm/L_Thal_05mm.bmv; /usr/share/fsl/5.0/bin/first_boundary_corr -s test-L_Amyg_first -o test-L_Amyg_corr -i anat_image -b fast
/usr/share/fsl/5.0/bin/run_first -i anat_image -t anat_image_to_std_sub.mat -n 30 -o test-L_Caud_first -m /usr/share/fsl/5.0/data/first/models_336_bin/intref_thal/L_Caud.bmv -intref /usr/share/fsl/5.0/data/first/models_336_bin/05mm/L_Thal_05mm.bmv; /usr/share/fsl/5.0/bin/first_boundary_corr -s test-L_Caud_first -o test-L_Caud_corr -i anat_image -b fast
/usr/share/fsl/5.0/bin/run_first -i anat_image -t anat_image_to_std_sub.mat -n 30 -o test-L_Hipp_first -m /usr/share/fsl/5.0/data/first/models_336_bin/intref_thal/L_Hipp.bmv -intref /usr/share/fsl/5.0/data/first/models_336_bin/05mm/L_Thal_05mm.bmv; /usr/share/fsl/5.0/bin/first_boundary_corr -s test-L_Hipp_first -o test-L_Hipp_corr -i anat_image -b fast
/usr/share/fsl/5.0/bin/run_first -i anat_image -t anat_image_to_std_sub.mat -n 40 -o test-L_Pall_first -m /usr/share/fsl/5.0/data/first/models_336_bin/05mm/L_Pall_05mm.bmv; /usr/share/fsl/5.0/bin/first_boundary_corr -s test-L_Pall_first -o test-L_Pall_corr -i anat_image -b none
/usr/share/fsl/5.0/bin/run_first -i anat_image -t anat_image_to_std_sub.mat -n 40 -o test-L_Puta_first -m /usr/share/fsl/5.0/data/first/models_336_bin/05mm/L_Puta_05mm.bmv; /usr/share/fsl/5.0/bin/first_boundary_corr -s test-L_Puta_first -o test-L_Puta_corr -i anat_image -b none
/usr/share/fsl/5.0/bin/run_first -i anat_image -t anat_image_to_std_sub.mat -n 40 -o test-L_Thal_first -m /usr/share/fsl/5.0/data/first/models_336_bin/05mm/L_Thal_05mm.bmv; /usr/share/fsl/5.0/bin/first_boundary_corr -s test-L_Thal_first -o test-L_Thal_corr -i anat_image -b none
/usr/share/fsl/5.0/bin/run_first -i anat_image -t anat_image_to_std_sub.mat -n 50 -o test-R_Accu_first -m /usr/share/fsl/5.0/data/first/models_336_bin/R_Accu_bin.bmv; /usr/share/fsl/5.0/bin/first_boundary_corr -s test-R_Accu_first -o test-R_Accu_corr -i anat_image -b fast
/usr/share/fsl/5.0/bin/run_first -i anat_image -t anat_image_to_std_sub.mat -n 50 -o test-R_Amyg_first -m /usr/share/fsl/5.0/data/first/models_336_bin/intref_thal/R_Amyg.bmv -intref /usr/share/fsl/5.0/data/first/models_336_bin/05mm/R_Thal_05mm.bmv; /usr/share/fsl/5.0/bin/first_boundary_corr -s test-R_Amyg_first -o test-R_Amyg_corr -i anat_image -b fast
/usr/share/fsl/5.0/bin/run_first -i anat_image -t anat_image_to_std_sub.mat -n 30 -o test-R_Caud_first -m /usr/share/fsl/5.0/data/first/models_336_bin/intref_thal/R_Caud.bmv -intref /usr/share/fsl/5.0/data/first/models_336_bin/05mm/R_Thal_05mm.bmv; /usr/share/fsl/5.0/bin/first_boundary_corr -s test-R_Caud_first -o test-R_Caud_corr -i anat_image -b fast
/usr/share/fsl/5.0/bin/run_first -i anat_image -t anat_image_to_std_sub.mat -n 30 -o test-R_Hipp_first -m /usr/share/fsl/5.0/data/first/models_336_bin/intref_thal/R_Hipp.bmv -intref /usr/share/fsl/5.0/data/first/models_336_bin/05mm/R_Thal_05mm.bmv; /usr/share/fsl/5.0/bin/first_boundary_corr -s test-R_Hipp_first -o test-R_Hipp_corr -i anat_image -b fast
/usr/share/fsl/5.0/bin/run_first -i anat_image -t anat_image_to_std_sub.mat -n 40 -o test-R_Pall_first -m /usr/share/fsl/5.0/data/first/models_336_bin/05mm/R_Pall_05mm.bmv; /usr/share/fsl/5.0/bin/first_boundary_corr -s test-R_Pall_first -o test-R_Pall_corr -i anat_image -b none
/usr/share/fsl/5.0/bin/run_first -i anat_image -t anat_image_to_std_sub.mat -n 40 -o test-R_Puta_first -m /usr/share/fsl/5.0/data/first/models_336_bin/05mm/R_Puta_05mm.bmv; /usr/share/fsl/5.0/bin/first_boundary_corr -s test-R_Puta_first -o test-R_Puta_corr -i anat_image -b none
/usr/share/fsl/5.0/bin/run_first -i anat_image -t anat_image_to_std_sub.mat -n 40 -o test-R_Thal_first -m /usr/share/fsl/5.0/data/first/models_336_bin/05mm/R_Thal_05mm.bmv; /usr/share/fsl/5.0/bin/first_boundary_corr -s test-R_Thal_first -o test-R_Thal_corr -i anat_image -b none
/usr/share/fsl/5.0/bin/run_first -i anat_image -t anat_image_to_std_sub.mat -n 40 -o test-BrStem_first -m /usr/share/fsl/5.0/data/first/models_336_bin/BrStem_bin.bmv; /usr/share/fsl/5.0/bin/first_boundary_corr -s test-BrStem_first -o test-BrStem_corr -i anat_image -b fast