diff --git a/modules/nf-neuro/preproc/eddy/main.nf b/modules/nf-neuro/preproc/eddy/main.nf index 1a70c5a..30e4fa1 100644 --- a/modules/nf-neuro/preproc/eddy/main.nf +++ b/modules/nf-neuro/preproc/eddy/main.nf @@ -20,7 +20,6 @@ process PREPROC_EDDY { task.ext.when == null || task.ext.when script: - def eddy_options = task.ext.args ? "--eddy_options \"$task.ext.args\"" : "" def prefix = task.ext.prefix ?: "${meta.id}" def slice_drop_flag = task.ext.slice_drop_correction ? "--slice_drop_correction " : "" def bet_topup_before_eddy_f = task.ext.bet_topup_before_eddy_f ?: "" @@ -74,7 +73,7 @@ process PREPROC_EDDY { --readout $readout --out_script --fix_seed\ --n_reverse \${number_rev_dwi}\ --lsr_resampling\ - $slice_drop_flag $eddy_options + $slice_drop_flag else scil_dwi_extract_b0.py \${dwi} \${bval} \${bvec} ${prefix}__b0.nii.gz --mean\ --b0_threshold $b0_thr_extract_b0 --skip_b0_check @@ -89,7 +88,7 @@ process PREPROC_EDDY { --eddy_cmd $eddy_cmd --b0_thr $b0_thr_extract_b0\ --encoding_direction $encoding\ --readout $readout --out_script --fix_seed\ - $slice_drop_flag $eddy_options + $slice_drop_flag fi echo "--very_verbose $extra_args" >> eddy.sh diff --git a/subworkflows/nf-neuro/tractoflow/modules.config b/subworkflows/nf-neuro/tractoflow/modules.config index 4dfb03c..458466d 100644 --- a/subworkflows/nf-neuro/tractoflow/modules.config +++ b/subworkflows/nf-neuro/tractoflow/modules.config @@ -33,7 +33,6 @@ process { ext.b0_thr_extract_b0 = params.dwi_b0_extract_threshold ext.encoding = "y" //FIXME : this is subject bound, pass through meta ? ext.readout = 0.062 //FIXME : this is subject bound, pass through meta ? - ext.args = params.dwi_motion_and_eddy_filter_command_args } withName: "TRACTOFLOW:PREPROC_DWI:BETCROP_FSLBETCROP" { diff --git a/subworkflows/nf-neuro/tractoflow/nextflow.config b/subworkflows/nf-neuro/tractoflow/nextflow.config index 043e072..da181dc 100644 --- a/subworkflows/nf-neuro/tractoflow/nextflow.config +++ b/subworkflows/nf-neuro/tractoflow/nextflow.config @@ -30,7 +30,6 @@ params { dwi_motion_and_eddy_filter_command = "eddy_cpu" dwi_motion_and_eddy_filter_bet_f_threshold = 0.16 dwi_motion_and_eddy_filter_restore_slices = true - dwi_motion_and_eddy_filter_command_args = "" //**Final DWI BET**// dwi_mask_final_bet_f_threshold = 0.16 diff --git a/subworkflows/nf-neuro/tractoflow/tests/main.nf.test b/subworkflows/nf-neuro/tractoflow/tests/main.nf.test index a6500f3..511e7bd 100644 --- a/subworkflows/nf-neuro/tractoflow/tests/main.nf.test +++ b/subworkflows/nf-neuro/tractoflow/tests/main.nf.test @@ -39,9 +39,8 @@ nextflow_workflow { test("tractoflow - no rev") { when { params { - dwi_motion_and_eddy_filter_command_args = "--fep" dwi_motion_and_eddy_filter_bet_f_threshold = 0.3 - dwi_mask_final_bet_f_threshold = 0.3 + dwi_mask_final_bet_f_threshold = 0.16 fodf_pft_fit_seeding_n_seeds = 1 fodf_pft_fit_filter_n_particles = 4 fodf_local_fit_seeding_n_seeds = 1 diff --git a/subworkflows/nf-neuro/tractoflow/tests/main.nf.test.snap b/subworkflows/nf-neuro/tractoflow/tests/main.nf.test.snap index 076afc4..8082058 100644 --- a/subworkflows/nf-neuro/tractoflow/tests/main.nf.test.snap +++ b/subworkflows/nf-neuro/tractoflow/tests/main.nf.test.snap @@ -15,7 +15,7 @@ { "id": "test" }, - "test__t1_warped.nii.gz:md5,8d02cdc310475e7d9f73ed7e61835f80" + "test__t1_warped.nii.gz:md5,e1d5080a5280df16a719c39825ce5ba2" ] ], "10": [ @@ -23,8 +23,8 @@ { "id": "test" }, - "test__output1Warp.nii.gz:md5,bab8ac8676cdca96f780eb1a93a254f2", - "test__output0GenericAffine.mat:md5,a8749c8f3e24dc98fa2299acf8076a88" + "test__output1Warp.nii.gz:md5,e4956aa73a6f497e5c316dfe24086fa9", + "test__output0GenericAffine.mat:md5,7ce31e1314d3f591b07eb5844e6cc237" ] ], "11": [ @@ -32,8 +32,8 @@ { "id": "test" }, - "test__output0GenericAffine.mat:md5,a8749c8f3e24dc98fa2299acf8076a88", - "test__output1InverseWarp.nii.gz:md5,74060775a192a4d051ee0dc26e309e65" + "test__output0GenericAffine.mat:md5,7ce31e1314d3f591b07eb5844e6cc237", + "test__output1InverseWarp.nii.gz:md5,532398bd5366613c4ceb71f09227a343" ] ], "12": [ @@ -41,7 +41,7 @@ { "id": "test" }, - "test_t1_cropped.nii.gz:md5,b31fd188e250502273f89c0c73c34628" + "test_t1_cropped.nii.gz:md5,c804e09ae12b053d76e10a3d74e98fb6" ] ], "13": [ @@ -105,7 +105,7 @@ { "id": "test" }, - "test__mask_wm.nii.gz:md5,82bf94c71fb31a2c73dd4ddc021b6d81" + "test__mask_wm.nii.gz:md5,d99f87e8fe4b713f85b8156bb00cb165" ] ], "20": [ @@ -189,7 +189,7 @@ { "id": "test" }, - "test__mask_gm.nii.gz:md5,444e4c93ed39418f015cca8711c7f3fc" + "test__mask_gm.nii.gz:md5,40756ebc4a82a284a170ad699e0a5e30" ] ], "30": [ @@ -246,7 +246,7 @@ { "id": "test" }, - "test__pft_tracking.trk:md5,9234bb8361568b22baebd47d050fcedf" + "test__pft_tracking.trk:md5,38b3f540d2f112d5bbf026416b3d27ec" ] ], "39": [ @@ -262,7 +262,7 @@ { "id": "test" }, - "test__mask_csf.nii.gz:md5,356b9cae3adb8579e17a8679a27117d3" + "test__mask_csf.nii.gz:md5,277db7da3c1ed92947c177edeb5eaa7d" ] ], "40": [ @@ -270,7 +270,7 @@ { "id": "test" }, - "test__map_include.nii.gz:md5,f6ab6cb53316ab7d4672230e20aa0ea8" + "test__map_include.nii.gz:md5,d9983cec6fe4dbc7becce71ffac237b8" ] ], "41": [ @@ -278,7 +278,7 @@ { "id": "test" }, - "test__map_exclude.nii.gz:md5,b41e6b0f1c5697856cba3669746e7b4d" + "test__map_exclude.nii.gz:md5,44839611fb77fd588e99b9afa0ae6b91" ] ], "42": [ @@ -286,7 +286,7 @@ { "id": "test" }, - "test__pft_seeding_mask.nii.gz:md5,1a824035733bd230eb82fd79c8ab6cdc" + "test__pft_seeding_mask.nii.gz:md5,3429293546e20469c84502394e37885d" ] ], "43": [ @@ -294,7 +294,7 @@ { "id": "test" }, - "test__local_tracking.trk:md5,53432f584dcceeaa4b95874905e21224" + "test__local_tracking.trk:md5,5bf9827570b27aa3eaf19f9d76bae764" ] ], "44": [ @@ -310,7 +310,7 @@ { "id": "test" }, - "test__local_seeding_mask.nii.gz:md5,82bf94c71fb31a2c73dd4ddc021b6d81" + "test__local_seeding_mask.nii.gz:md5,d99f87e8fe4b713f85b8156bb00cb165" ] ], "46": [ @@ -318,7 +318,7 @@ { "id": "test" }, - "test__local_tracking_mask.nii.gz:md5,82bf94c71fb31a2c73dd4ddc021b6d81" + "test__local_tracking_mask.nii.gz:md5,d99f87e8fe4b713f85b8156bb00cb165" ] ], "47": [ @@ -350,7 +350,7 @@ { "id": "test" }, - "test__map_wm.nii.gz:md5,c1fa90c2f2687dc206ee681a3420c525" + "test__map_wm.nii.gz:md5,cd10401b5feee8c2bc531b34612ac959" ] ], "50": [ @@ -378,7 +378,7 @@ { "id": "test" }, - "test__map_gm.nii.gz:md5,2fcc377353a21f697878d8e45b2dc2c1" + "test__map_gm.nii.gz:md5,9ea2161ff256ba6680db86c28624191a" ] ], "7": [ @@ -386,7 +386,7 @@ { "id": "test" }, - "test__map_csf.nii.gz:md5,9c5cc395eeaffd3ec7a7f9baa07122cc" + "test__map_csf.nii.gz:md5,68f53afcc61f09d70484665161415aa8" ] ], "8": [ @@ -424,8 +424,8 @@ { "id": "test" }, - "test__output1Warp.nii.gz:md5,bab8ac8676cdca96f780eb1a93a254f2", - "test__output0GenericAffine.mat:md5,a8749c8f3e24dc98fa2299acf8076a88" + "test__output1Warp.nii.gz:md5,e4956aa73a6f497e5c316dfe24086fa9", + "test__output0GenericAffine.mat:md5,7ce31e1314d3f591b07eb5844e6cc237" ] ], "aparc_aseg": [ @@ -439,7 +439,7 @@ { "id": "test" }, - "test__map_csf.nii.gz:md5,9c5cc395eeaffd3ec7a7f9baa07122cc" + "test__map_csf.nii.gz:md5,68f53afcc61f09d70484665161415aa8" ] ], "csf_mask": [ @@ -447,7 +447,7 @@ { "id": "test" }, - "test__mask_csf.nii.gz:md5,356b9cae3adb8579e17a8679a27117d3" + "test__mask_csf.nii.gz:md5,277db7da3c1ed92947c177edeb5eaa7d" ] ], "diffusion_to_anatomical": [ @@ -455,8 +455,8 @@ { "id": "test" }, - "test__output0GenericAffine.mat:md5,a8749c8f3e24dc98fa2299acf8076a88", - "test__output1InverseWarp.nii.gz:md5,74060775a192a4d051ee0dc26e309e65" + "test__output0GenericAffine.mat:md5,7ce31e1314d3f591b07eb5844e6cc237", + "test__output1InverseWarp.nii.gz:md5,532398bd5366613c4ceb71f09227a343" ] ], "dti_ad": [ @@ -620,7 +620,7 @@ { "id": "test" }, - "test__map_gm.nii.gz:md5,2fcc377353a21f697878d8e45b2dc2c1" + "test__map_gm.nii.gz:md5,9ea2161ff256ba6680db86c28624191a" ] ], "gm_mask": [ @@ -628,7 +628,7 @@ { "id": "test" }, - "test__mask_gm.nii.gz:md5,444e4c93ed39418f015cca8711c7f3fc" + "test__mask_gm.nii.gz:md5,40756ebc4a82a284a170ad699e0a5e30" ] ], "local_config": [ @@ -644,7 +644,7 @@ { "id": "test" }, - "test__local_seeding_mask.nii.gz:md5,82bf94c71fb31a2c73dd4ddc021b6d81" + "test__local_seeding_mask.nii.gz:md5,d99f87e8fe4b713f85b8156bb00cb165" ] ], "local_tracking_mask": [ @@ -652,7 +652,7 @@ { "id": "test" }, - "test__local_tracking_mask.nii.gz:md5,82bf94c71fb31a2c73dd4ddc021b6d81" + "test__local_tracking_mask.nii.gz:md5,d99f87e8fe4b713f85b8156bb00cb165" ] ], "local_tractogram": [ @@ -660,7 +660,7 @@ { "id": "test" }, - "test__local_tracking.trk:md5,53432f584dcceeaa4b95874905e21224" + "test__local_tracking.trk:md5,5bf9827570b27aa3eaf19f9d76bae764" ] ], "nonphysical_voxels": [ @@ -692,7 +692,7 @@ { "id": "test" }, - "test__map_exclude.nii.gz:md5,b41e6b0f1c5697856cba3669746e7b4d" + "test__map_exclude.nii.gz:md5,44839611fb77fd588e99b9afa0ae6b91" ] ], "pft_map_include": [ @@ -700,7 +700,7 @@ { "id": "test" }, - "test__map_include.nii.gz:md5,f6ab6cb53316ab7d4672230e20aa0ea8" + "test__map_include.nii.gz:md5,d9983cec6fe4dbc7becce71ffac237b8" ] ], "pft_seeding_mask": [ @@ -708,7 +708,7 @@ { "id": "test" }, - "test__pft_seeding_mask.nii.gz:md5,1a824035733bd230eb82fd79c8ab6cdc" + "test__pft_seeding_mask.nii.gz:md5,3429293546e20469c84502394e37885d" ] ], "pft_tractogram": [ @@ -716,7 +716,7 @@ { "id": "test" }, - "test__pft_tracking.trk:md5,9234bb8361568b22baebd47d050fcedf" + "test__pft_tracking.trk:md5,38b3f540d2f112d5bbf026416b3d27ec" ] ], "pulsation_in_b0": [ @@ -740,7 +740,7 @@ { "id": "test" }, - "test__t1_warped.nii.gz:md5,8d02cdc310475e7d9f73ed7e61835f80" + "test__t1_warped.nii.gz:md5,e1d5080a5280df16a719c39825ce5ba2" ] ], "t1_native": [ @@ -748,7 +748,7 @@ { "id": "test" }, - "test_t1_cropped.nii.gz:md5,b31fd188e250502273f89c0c73c34628" + "test_t1_cropped.nii.gz:md5,c804e09ae12b053d76e10a3d74e98fb6" ] ], "versions": [ @@ -774,7 +774,7 @@ { "id": "test" }, - "test__map_wm.nii.gz:md5,c1fa90c2f2687dc206ee681a3420c525" + "test__map_wm.nii.gz:md5,cd10401b5feee8c2bc531b34612ac959" ] ], "wm_mask": [ @@ -782,7 +782,7 @@ { "id": "test" }, - "test__mask_wm.nii.gz:md5,82bf94c71fb31a2c73dd4ddc021b6d81" + "test__mask_wm.nii.gz:md5,d99f87e8fe4b713f85b8156bb00cb165" ] ], "wmparc": [ @@ -794,6 +794,6 @@ "nf-test": "0.9.0", "nextflow": "24.10.2" }, - "timestamp": "2024-12-17T19:37:33.475410485" + "timestamp": "2024-12-18T22:11:36.11074401" } } \ No newline at end of file