diff --git a/nextflow.config b/nextflow.config index 887283e..7ae23de 100644 --- a/nextflow.config +++ b/nextflow.config @@ -30,6 +30,7 @@ params { // FODF || QBALL use_fodf_for_tracking = false sh_order = 6 + min_fodf_value = 1000 // Tracking run_tracking = true @@ -403,6 +404,45 @@ process { ext.max_dti_shell_value = params.max_dti_shell_value } +withName: "RECONST_FODF" { + ext.sh_order = 6 + ext.sh_basis = "descoteaux07" + ext.fa_threshold = 0.1 + ext.md_threshold = 0.003 + ext.relative_threshold = 0.1 + ext.absolute_peaks = true + ext.peaks = true + ext.peak_values = true + ext.peak_indices = true + ext.afd_max = true + ext.afd_total = true + ext.afd_sum = true + ext.nufo = true + ext.b0_thr_extract_b0 = params.b0_threshold + ext.min_fodf_shell_value = params.min_fodf_value + publishDir = [ + path: { "${params.outdir}/${meta.id}/dwi/"}, + saveAs: { + filename -> + if ( filename.contains("fodf.nii.gz") ) { "${meta.id}_model-csd_param-fodf_dwimap.nii.gz" } + else if ( filename.contains("wm.nii.gz") ) { "${meta.id}_model-csd_param-wm_dwimap.nii.gz" } + else if ( filename.contains("gm.nii.gz") ) { "${meta.id}_model-csd_param-gm_dwimap.nii.gz" } + else if ( filename.contains("csf.nii.gz") ) { "${meta.id}_model-csd_param-csf_dwimap.nii.gz" } + else if ( filename.contains("vf.nii.gz") ) { "${meta.id}_model-csd_param-vf_dwimap.nii.gz" } + else if ( filename.contains("vf_rgb.nii.gz") ) { "${meta.id}_model-csd_param-rgb_dwimap.nii.gz" } + else if ( filename.contains("afd_total.nii.gz") ) { "${meta.id}_model-csd_param-afdtot_dwimap.nii.gz" } + else if ( filename.contains("afd_sum.nii.gz") ) { "${meta.id}_model-csd_param-afdsum_dwimap.nii.gz" } + else if ( filename.contains("afd_max.nii.gz") ) { "${meta.id}_model-csd_param-afdmax_dwimap.nii.gz" } + else if ( filename.contains("nufo.nii.gz") ) { "${meta.id}_model-csf_csd_param-nufo_dwimap.nii.gz" } + else if ( filename.contains("evecs_v1.nii.gz") ) { "${meta.id}_model-csd_param-v1_dwimap.nii.gz" } + else if ( filename.contains("evecs_v2.nii.gz") ) { "${meta.id}_model-csd_param-v2_dwimap.nii.gz" } + else if ( filename.contains("evecs_v3.nii.gz") ) { "${meta.id}_model-csd_param-v3_dwimap.nii.gz" } + else if ( filename.contains("versions.yml") ) { null } + else { params.lean_output ? null : filename } + } + ] + } + withName: "RECONST_QBALL" { ext.sh_order = params.sh_order ext.qball = true