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Fodf optional #32

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a7b6b6d
fodf optional step
EliseCos Dec 12, 2025
24ffd36
add sentence
EliseCos Dec 12, 2025
7516cb4
Update file nextflow_schema.json
EliseCos Dec 13, 2025
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7 changes: 6 additions & 1 deletion main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -68,6 +68,10 @@ workflow {
if ( params.use_fodf_for_tracking && ! params.run_tracking ) {
error "The parameter use_fodf_for_tracking cannot be enabled if run_tracking is disabled."
}

if ( params.use_fodf_for_tracking && ! params.run_fodf) {
error "The parameter use_fodf_for_tracking cannot be enabled if run_fodf is disabled."
}

ch_dwi_bvalbvec = data.dwi
.multiMap { meta, dwi, bval, bvec ->
Expand Down Expand Up @@ -167,14 +171,15 @@ workflow {
ch_multiqc_files = ch_multiqc_files.mix(RECONST_DTIMETRICS.out.mqc)

/* FODF */
if ( params.run_fodf ) {
RECONST_FRF(ch_for_reconst.map{ it + [[], [], []]})
ch_for_reconst_fodf = ch_for_reconst
.join(RECONST_DTIMETRICS.out.fa)
.join(RECONST_DTIMETRICS.out.md)
.join(RECONST_FRF.out.frf)
.map{ it + [[], []]}
RECONST_FODF(ch_for_reconst_fodf)

}
Comment on lines +174 to +182
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@arnaudbore arnaudbore Dec 13, 2025

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Suggested change
if ( params.run_fodf ) {
RECONST_FRF(ch_for_reconst.map{ it + [[], [], []]})
ch_for_reconst_fodf = ch_for_reconst
.join(RECONST_DTIMETRICS.out.fa)
.join(RECONST_DTIMETRICS.out.md)
.join(RECONST_FRF.out.frf)
.map{ it + [[], []]}
RECONST_FODF(ch_for_reconst_fodf)
}
if ( params.run_fodf ) {
RECONST_FRF(ch_for_reconst.map{ it + [[], [], []]})
ch_for_reconst_fodf = ch_for_reconst
.join(RECONST_DTIMETRICS.out.fa)
.join(RECONST_DTIMETRICS.out.md)
.join(RECONST_FRF.out.frf)
.map{ it + [[], []]}
RECONST_FODF(ch_for_reconst_fodf)
}

/* QBALL */
RECONST_QBALL(ch_for_reconst)

Expand Down
1 change: 1 addition & 0 deletions nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,7 @@ params {
nvox_min = 100

// FODF || QBALL
run_fodf = true
use_fodf_for_tracking = false
sh_order = 6
min_fodf_value = 1000
Expand Down
6 changes: 6 additions & 0 deletions nextflow_schema.json
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Expand Up @@ -90,6 +90,12 @@
"description": "Set it to false if you don't want to resample your data to the smallest current voxel dimension.",
"fa_icon": "fas fa-brain"
},
"run_fodf": {
"type": "boolean",
"default": true,
"description": "Set it to false if you don't want to run fODF",
"fa_icon": "fas fa-brain"
},
"run_tracking": {
"type": "boolean",
"default": true,
Expand Down