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more metadata, added test, fix to modules and more configuration
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| Original file line number | Diff line number | Diff line change |
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| process { | ||
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| /* SUBWORKFLOWS CONFIGURATION */ | ||
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| withName: "TRACTOFLOW:PREPROC_DWI:DENOISE_DWI" { | ||
| ext.extent = params.dwi_noise_filter_patch_size | ||
| } | ||
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| withName: "TRACTOFLOW:PREPROC_DWI:DENOISE_REVDWI" { | ||
| ext.extent = params.dwi_noise_filter_patch_size | ||
| } | ||
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| withName: "TRACTOFLOW:PREPROC_DWI:TOPUP_EDDY:UTILS_EXTRACTB0" { | ||
| ext.b0_extraction_strategy = "mean" | ||
| } | ||
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| withName: "TRACTOFLOW:PREPROC_DWI:TOPUP_EDDY:PREPROC_TOPUP" { | ||
| ext.prefix_topup = params.dwi_susceptibility_filter_output_prefix | ||
| ext.default_config_topup = params.dwi_susceptibility_filter_config_file | ||
| ext.encoding = "y" //FIXME : this is subject bound, pass through meta ? | ||
| ext.readout = 0.062 //FIXME : this is subject bound, pass through meta ? | ||
| ext.b0_thr_extract_b0 = params.dwi_b0_extract_threshold | ||
| } | ||
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| withName: "TRACTOFLOW:PREPROC_DWI:TOPUP_EDDY:PREPROC_EDDY" { | ||
| ext.prefix_topup = params.dwi_susceptibility_filter_output_prefix | ||
| ext.slice_drop_flag = params.dwi_motion_and_eddy_filter_restore_slices | ||
| ext.bet_topup_before_eddy_f = params.dwi_motion_and_eddy_filter_bet_f_threshold | ||
| ext.eddy_cmd = params.dwi_motion_and_eddy_filter_command | ||
| ext.dilate_b0_mask_prelim_brain_extraction = params.dwi_mask_prelim_bet_dilation_radius | ||
| ext.bet_prelim_f = params.dwi_mask_prelim_bet_f_threshold | ||
| 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 | ||
| } | ||
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| withName: "TRACTOFLOW:PREPROC_DWI:BETCROP_FSLBETCROP" { | ||
| ext.bet_f = params.dwi_mask_final_bet_f_threshold | ||
| ext.b0_thr = params.dwi_b0_extract_threshold | ||
| ext.crop = true | ||
| ext.dilate = false | ||
| } | ||
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| withName: "TRACTOFLOW:PREPROC_DWI:N4_DWI" { | ||
| ext.bspline_knot_per_voxel = params.dwi_intensities_normalize_density | ||
| ext.shrink_factor = params.dwi_intensities_normalize_subsampling | ||
| } | ||
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| withName: "TRACTOFLOW:PREPROC_DWI:RESAMPLE_DWI" { | ||
| ext.voxel_size = params.dwi_spatial_resample_resolution | ||
| ext.interp = params.dwi_spatial_resample_interpolation | ||
| ext.first_suffix = "dwi" | ||
| } | ||
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| withName: "TRACTOFLOW:PREPROC_DWI:BETCROP_CROPVOLUME" { | ||
| ext.output_bbox = false | ||
| } | ||
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| withName: "TRACTOFLOW:PREPROC_DWI:RESAMPLE_MASK" { | ||
| ext.voxel_size = params.dwi_spatial_resample_resolution | ||
| ext.interp = "nn" | ||
| ext.first_suffix = "dwi_mask" | ||
| } | ||
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| withName: "TRACTOFLOW:PREPROC_T1:BETCROP_CROPVOLUME_T1" { | ||
| ext.output_bbox = true | ||
| ext.first_suffix = "t1" | ||
| } | ||
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| withName: "TRACTOFLOW:PREPROC_T1:IMAGE_RESAMPLE" { | ||
| ext.voxel_size = params.t1_spatial_resample_resolution | ||
| ext.interp = params.t1_spatial_resample_interpolation | ||
| ext.first_suffix = "t1" | ||
| } | ||
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| //withName: "TRACTOFLOW:T1_REGISTRATION:REGISTER_ANATTODWI" { | ||
| // Nothing to do ! | ||
| //} | ||
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| //withName: "TRACTOFLOW:ANATOMICAL_SEGMENTATION:SEGMENTATION_FASTSEG" { | ||
| // Nothing to do ! | ||
| //} | ||
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| //withName: "TRACTOFLOW:ANATOMICAL_SEGMENTATION:SEGMENTATION_FREESURFERSEG" { | ||
| // Nothing to do ! | ||
| //} | ||
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| /* MODULES CONFIGURATION */ | ||
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| withName: "TRACTOFLOW:REGISTRATION_FA" { | ||
| ext.fa = true | ||
| ext.ad = false | ||
| ext.evecs = false | ||
| ext.evals = false | ||
| ext.ga = false | ||
| ext.rgb = false | ||
| ext.md = false | ||
| ext.mode = false | ||
| ext.norm = false | ||
| ext.rd = false | ||
| ext.tensor = false | ||
| ext.nonphysical = false | ||
| ext.pulsation = false | ||
| ext.residual = false | ||
| } | ||
|
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| withName: "TRACTOFLOW:TRANSFORM_WMPARC" { | ||
| ext.dimensionality = 3 | ||
| ext.image_type = 0 | ||
| ext.interpolation = "NearestNeighbor" | ||
| ext.output_dtype = "uchar" | ||
| ext.default_val = 0 | ||
| } | ||
|
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| withName: "TRACTOFLOW:TRANSFORM_APARC_ASEG" { | ||
| ext.dimensionality = 3 | ||
| ext.image_type = 0 | ||
| ext.interpolation = "MultiLabel" | ||
| ext.output_dtype = "short" | ||
| ext.default_val = 0 | ||
| } | ||
|
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| withName: "TRACTOFLOW:RECONST_FRF" { | ||
| ext.fa = params.dwi_fodf_fit_frf_max_fa_threshold | ||
| ext.fa_min = params.dwi_fodf_fit_frf_min_fa_threshold | ||
| ext.nvox_min = params.dwi_fodf_fit_frf_min_n_voxels | ||
| ext.roi_radius = params.dwi_fodf_fit_frf_roi_radius | ||
| ext.set_frf = params.dwi_fodf_fit_force_frf ? true : false | ||
| ext.manual_frf = params.dwi_fodf_fit_force_frf | ||
| } | ||
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| //withName: "RECONST_MEANFRF" { | ||
| // Nothing to do ! | ||
| //} | ||
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| withName: "TRACTOFLOW:RECONST_DTIMETRICS" { | ||
| ext.ad = true | ||
| ext.evecs = true | ||
| ext.evals = true | ||
| ext.fa = true | ||
| ext.ga = true | ||
| ext.rgb = true | ||
| ext.md = true | ||
| ext.mode = true | ||
| ext.norm = true | ||
| ext.rd = true | ||
| ext.tensor = true | ||
| ext.nonphysical = true | ||
| ext.pulsation = true | ||
| ext.residual = true | ||
| } | ||
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| withName: "TRACTOFLOW:RECONST_FODF" { | ||
| ext.b0_thr_extract_b0 = params.dwi_b0_extract_threshold | ||
| ext.dwi_shell_tolerance = params.dwi_shell_extract_tolerance | ||
| ext.min_fodf_shell_value = params.dwi_fodf_fit_shell_min_bval | ||
| ext.fodf_shells = params.dwi_fodf_fit_shells | ||
| ext.sh_order = params.dwi_fodf_fit_order | ||
| ext.sh_basis = params.dwi_fodf_fit_basis | ||
| ext.fa_threshold = params.dwi_fodf_fit_peaks_ventricle_max_fa | ||
| ext.md_threshold = params.dwi_fodf_fit_peaks_ventricle_min_md | ||
| ext.relative_threshold = params.dwi_fodf_fit_peaks_relative_threshold | ||
| ext.fodf_metrics_a_factor = params.dwi_fodf_fit_peaks_absolute_factor | ||
| ext.absolute_peaks = true | ||
| ext.peaks = true | ||
| ext.peak_indices = true | ||
| ext.afd_max = true | ||
| ext.afd_total = true | ||
| ext.afd_sum = true | ||
| ext.nufo = true | ||
| } | ||
|
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| withName: "TRACTOFLOW:TRACKING_PFTTRACKING" { | ||
| ext.pft_seeding_mask_type = params.fodf_pft_fit_seeding_type | ||
| ext.pft_fa_seeding_mask_threshold = params.fodf_pft_fit_seeding_fa_mask_threshold | ||
| ext.pft_seeding = params.fodf_pft_fit_seeding_strategy | ||
| ext.pft_nbr_seeds = params.fodf_pft_fit_seeding_n_seeds | ||
| ext.pft_algo = params.fodf_pft_fit_algorithm | ||
| ext.pft_step = params.fodf_pft_fit_step_size | ||
| ext.pft_theta = params.fodf_pft_fit_theta_max_deviation | ||
| ext.pft_sfthres = params.fodf_pft_fit_sf_threshold | ||
| ext.pft_sfthres_init = params.fodf_pft_fit_sf_initial_threshold | ||
| ext.pft_min_len = params.fodf_pft_fit_streamline_min_length | ||
| ext.pft_max_len = params.fodf_pft_fit_streamline_max_length | ||
| ext.pft_particles = params.fodf_pft_fit_filter_n_particles | ||
| ext.pft_back = params.fodf_pft_fit_filter_backward_step_size | ||
| ext.pft_front = params.fodf_pft_fit_filter_forward_step_size | ||
| ext.pft_random_seed = params.fodf_pft_fit_random_seed | ||
| ext.pft_compress_streamlines = params.fodf_pft_fit_compress_tractogram | ||
| ext.pft_compress_value = params.fodf_pft_fit_compress_max_displacement | ||
| ext.basis = params.dwi_fodf_fit_basis | ||
| } | ||
|
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| withName: "TRACTOFLOW:TRACKING_LOCALTRACKING" { | ||
| ext.local_tracking_mask_type = params.fodf_local_fit_tracking_mask_type | ||
| ext.local_fa_tracking_mask_threshold = params.fodf_local_fit_tracking_mask_fa_threshold | ||
| ext.local_seeding_mask_type = params.fodf_local_fit_seeding_type | ||
| ext.local_fa_seeding_mask_threshold = params.fodf_local_fit_seeding_fa_threshold | ||
| ext.local_seeding = params.fodf_local_fit_seeding_strategy | ||
| ext.local_nbr_seeds = params.fodf_local_fit_seeding_n_seeds | ||
| ext.local_algo = params.fodf_local_fit_algorithm | ||
| ext.local_step = params.fodf_local_fit_step_size | ||
| ext.local_theta = params.fodf_local_fit_theta_max_deviation | ||
| ext.local_sfthres = params.fodf_local_fit_sf_threshold | ||
| ext.local_min_len = params.fodf_local_fit_streamline_min_length | ||
| ext.local_max_len = params.fodf_local_fit_streamline_max_length | ||
| ext.local_random_seed = params.fodf_local_fit_random_seed | ||
| ext.local_compress_streamlines = params.fodf_local_fit_compress_tractogram | ||
| ext.local_compress_value = params.fodf_local_fit_compress_max_displacement | ||
| ext.basis = params.dwi_fodf_fit_basis | ||
| } | ||
| } |
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