Messing around with Apptainer (formerly Singularity) containers
Version: Apptainer 1.5
singularity run
-B $PWD/token_dataset:/token_dataset:ro
-B $PWD/token_rabies_outputs:/token_rabies_outputs/ /scratch/ropdav/projects/singularity-testing/rabies_0.4.8.sif -p MultiProc --local_threads 6
preprocess /token_dataset/ /token_rabies_outputs
--anatomical_resampling 1x1x1
--anat_inho_cor method=disable,otsu_thresh=2,multiotsu=false --bold_inho_cor method=disable,otsu_thresh=2,multiotsu=false
--bold2anat_coreg registration=no_reg,masking=true,brain_extraction=true
--commonspace_reg masking=false,brain_extraction=false,fast_commonspace=true,template_registration=no_reg --data_type int16
singularity run
-B $PWD/token_dataset:/token_dataset:ro
-B $PWD/token_rabies_outputs:/token_rabies_outputs/ /scratch/ropdav/projects/singularity-testing/rabies_0.4.8.sif -p MultiProc --local_threads 6
confound_correction /token_rabies_outputs/ /token_rabies_outputs --conf_list mot_6
singularity run
-B $PWD/token_dataset:/token_dataset:ro
-B $PWD/token_rabies_outputs:/token_rabies_outputs/ /scratch/ropdav/projects/singularity-testing/rabies_0.4.8.sif -p MultiProc --local_threads 6
analysis /token_rabies_outputs/ /token_rabies_outputs --data_diagnosis
singularity run
-B $PWD/test_dataset:/test_dataset:ro
-B $PWD/test_dataset_outputs:/test_dataset_outputs/
gabdesgreg/rabies:0.4.8 -p MultiProc --local_threads 4
confound_correction /test_dataset_outputs/ /test_dataset_outputs
--frame_censoring FD_censoring=true,FD_threshold=0.05,DVARS_censoring=false,minimum_timepoint=80
--conf_list mot_6 WM_signal CSF_signal --smoothing_filter 0.3
singularity run
-B $PWD/test_dataset:/scratch/ropdav/projects/forks/test_nipoppy/extra-stuff/Rabies-preprocess-stuff/0.5.1/output:ro
-B $PWD/test_dataset_outputs:/scratch/ropdav/projects/forks/test_nipoppy/extra-stuff/rabies-confound-data/
rabies.sif -p MultiProc --local_threads 4
confound_correction /test_dataset_outputs/ /test_dataset_outputs
--frame_censoring FD_censoring=true,FD_threshold=0.05,DVARS_censoring=false,minimum_timepoint=80
--conf_list mot_6 WM_signal CSF_signal --smoothing_filter 0.3