Skip to content

add ouputs fodf .config #29

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
arnaudbore merged 2 commits into from
Nov 26, 2025
Merged

add ouputs fodf .config #29

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
9812ade
add ouputs fodf .config
EliseCos Nov 25, 2025
9e857fc
remove command run fodf
EliseCos Nov 26, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
40 changes: 40 additions & 0 deletions nextflow.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,7 @@ params {
// FODF || QBALL
use_fodf_for_tracking = false
sh_order = 6
min_fodf_value = 1000

// Tracking
run_tracking = true
Expand Down Expand Up @@ -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
Expand Down