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improve readability
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@AlexVCaron
AlexVCaron committed Dec 2, 2024
1 parent a1a3d93 commit 3ef944f
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76 changes: 49 additions & 27 deletions subworkflows/nf-neuro/preproc_dwi/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -14,61 +14,78 @@ include { TOPUP_EDDY } from '../topup_eddy/main'
workflow PREPROC_DWI {

take:
ch_dwi // channel: [ val(meta), [ dwi, bval, bvec ] ]
ch_rev_dwi // channel: [ val(meta), [ rev_dwi, bval, bvec ] ], optional
ch_b0 // Channel: [ val(meta), [ b0 ] ], optional
ch_rev_b0 // channel: [ val(meta), [ reverse b0 ] ], optional
ch_config_topup // channel: [ 'config_topup' ], optional
ch_dwi // channel: [ val(meta), dwi, bval, bvec ]
ch_rev_dwi // channel: [ val(meta), rev-dwi, bval, bvec ], optional
ch_b0 // Channel: [ val(meta), b0 ], optional
ch_rev_b0 // channel: [ val(meta), rev-b0 ], optional
ch_config_topup // channel: [ 'topup.cnf' ], optional

main:

ch_versions = Channel.empty()

ch_denoise_dwi = ch_dwi
ch_dwi_bvalbvec = ch_dwi
.multiMap { meta, dwi, bval, bvec ->
dwi: [ meta, dwi ]
bvs_files: [ meta, bval, bvec ]
}

// ** Denoised DWI ** //
DENOISE_DWI ( ch_denoise_dwi.dwi.map{ it + [[]] } )
ch_versions = ch_versions.mix(DENOISE_DWI.out.versions.first())

ch_denoise_rev_dwi = ch_rev_dwi
ch_rev_dwi_bvalbvec = ch_rev_dwi
.multiMap { meta, dwi, bval, bvec ->
rev_dwi: [ [id: "${meta.id}_rev", cache: meta], dwi ]
rev_dwi: [ meta, dwi ]
rev_bvs_files: [ meta, bval, bvec ]
}

DENOISE_REVDWI ( ch_denoise_rev_dwi.rev_dwi.map{ it + [[]] } )
// ** Denoise DWI ** //
ch_denoise_dwi = ch_dwi_bvalbvec.dwi
.map{ it + [[]] }

DENOISE_DWI ( ch_denoise_dwi )
ch_versions = ch_versions.mix(DENOISE_DWI.out.versions.first())

// ** Denoise REV-DWI ** //
// Need to append "rev" to the ID, to ensure output filenames
// are different from the DWI and prevent file collisions
// - "cache: meta" is used to save the "real" metadata with valid ID for
// join operations, so it can be recovered after execution
ch_denoise_rev_dwi = ch_rev_dwi_bvalbvec.rev_dwi
.map{ meta, dwi -> [ [id: "${meta.id}_rev", cache: meta], dwi, [] ] }

DENOISE_REVDWI ( ch_denoise_rev_dwi )
ch_versions = ch_versions.mix(DENOISE_REVDWI.out.versions.first())

// ** Eddy Topup ** //
ch_topup_eddy_dwi = DENOISE_DWI.out.image
.join(ch_dwi_bvalbvec.bvs_files)

// Recover the "real" ID from "meta[cache]" (see above), to join with the bval/bvec
ch_topup_eddy_rev_dwi = DENOISE_REVDWI.out.image
.map{ meta, dwi -> [ meta.cache, dwi ] }
.join(ch_denoise_rev_dwi.rev_bvs_files)
.join(ch_rev_dwi_bvalbvec.rev_bvs_files)

// ** Eddy Topup ** //
ch_topup_eddy_dwi = DENOISE_DWI.out.image.join(ch_denoise_dwi.bvs_files)
TOPUP_EDDY ( ch_topup_eddy_dwi, ch_b0, ch_topup_eddy_rev_dwi, ch_rev_b0, ch_config_topup )
ch_versions = ch_versions.mix(TOPUP_EDDY.out.versions.first())

// ** Bet-crop DWI ** //
ch_betcrop_dwi = TOPUP_EDDY.out.dwi
.join(TOPUP_EDDY.out.bval)
.join(TOPUP_EDDY.out.bvec)

BETCROP_FSLBETCROP ( ch_betcrop_dwi )
ch_versions = ch_versions.mix(BETCROP_FSLBETCROP.out.versions.first())

// ** Crop b0 ** //
ch_crop_b0 = TOPUP_EDDY.out.b0
.join(BETCROP_FSLBETCROP.out.bbox)

BETCROP_CROPVOLUME ( ch_crop_b0 )
ch_versions = ch_versions.mix(BETCROP_CROPVOLUME.out.versions.first())

// ** N4 DWI ** //
ch_N4 = BETCROP_FSLBETCROP.out.image
.join(BETCROP_CROPVOLUME.out.image)
.join(BETCROP_FSLBETCROP.out.mask)

N4_DWI ( ch_N4 )
ch_versions = ch_versions.mix(N4_DWI.out.versions.first())

Expand All @@ -77,11 +94,14 @@ workflow PREPROC_DWI {
.join(TOPUP_EDDY.out.bval)
.join(TOPUP_EDDY.out.bvec)
.join(BETCROP_FSLBETCROP.out.mask)

NORMALIZE_DWI ( ch_normalize )
ch_versions = ch_versions.mix(NORMALIZE_DWI.out.versions.first())

// ** Resample DWI ** //
ch_resample_dwi = NORMALIZE_DWI.out.dwi.map{ it + [[]] }
ch_resample_dwi = NORMALIZE_DWI.out.dwi
.map{ it + [[]] }

RESAMPLE_DWI ( ch_resample_dwi )
ch_versions = ch_versions.mix(RESAMPLE_DWI.out.versions.first())

Expand All @@ -94,18 +114,20 @@ workflow PREPROC_DWI {
ch_versions = ch_versions.mix(EXTRACTB0_RESAMPLE.out.versions.first())

// ** Resample mask ** //
ch_resample_mask = BETCROP_FSLBETCROP.out.mask.map{ it + [[]] }
ch_resample_mask = BETCROP_FSLBETCROP.out.mask
.map{ it + [[]] }

RESAMPLE_MASK ( ch_resample_mask )
ch_versions = ch_versions.mix(RESAMPLE_MASK.out.versions.first())

emit:
dwi_resample = RESAMPLE_DWI.out.image // channel: [ val(meta), [ dwi_resample ] ]
bval = TOPUP_EDDY.out.bval // channel: [ val(meta), [ bval_corrected ] ]
bvec = TOPUP_EDDY.out.bvec // channel: [ val(meta), [ bvec_corrected ] ]
b0 = EXTRACTB0_RESAMPLE.out.b0 // channel: [ val(meta), [ b0 ] ]
b0_mask = RESAMPLE_MASK.out.image // channel: [ val(meta), [ b0_mask ] ]
dwi_bounding_box = BETCROP_FSLBETCROP.out.bbox // channel: [ val(meta), [ dwi_bounding_box ] ]
dwi_topup_eddy = TOPUP_EDDY.out.dwi // channel: [ val(meta), [ dwi_topup_eddy ] ]
dwi_n4 = N4_DWI.out.image // channel: [ val(meta), [ dwi_n4 ] ]
versions = ch_versions // channel: [ versions.yml ]
dwi_resample = RESAMPLE_DWI.out.image // channel: [ val(meta), dwi-resampled ]
bval = TOPUP_EDDY.out.bval // channel: [ val(meta), bval-corrected ]
bvec = TOPUP_EDDY.out.bvec // channel: [ val(meta), bvec-corrected ]
b0 = EXTRACTB0_RESAMPLE.out.b0 // channel: [ val(meta), b0-resampled ]
b0_mask = RESAMPLE_MASK.out.image // channel: [ val(meta), b0-mask ]
dwi_bounding_box = BETCROP_FSLBETCROP.out.bbox // channel: [ val(meta), dwi-bounding-box ]
dwi_topup_eddy = TOPUP_EDDY.out.dwi // channel: [ val(meta), dwi-after-topup-eddy ]
dwi_n4 = N4_DWI.out.image // channel: [ val(meta), dwi-after-n4 ]
versions = ch_versions // channel: [ versions.yml ]
}
46 changes: 24 additions & 22 deletions subworkflows/nf-neuro/topup_eddy/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -9,25 +9,26 @@ workflow TOPUP_EDDY {
// ** In both cases, it will perform EDDY and also extract a b0 from the corrected DWI image. ** //

take:
ch_dwi // channel: [ val(meta), [ dwi, bval, bvec ]
ch_b0 // channel: [ val(meta), b0 ]
ch_rev_dwi // channel: [ val(meta), [ rev_dwi, rev_bval, rev_bvec ]
ch_rev_b0 // channel: [ val(meta), rev_b0 ]
ch_config_topup // channel
ch_dwi // channel: [ val(meta), dwi, bval, bvec ]
ch_b0 // channel: [ val(meta), b0 ], optional
ch_rev_dwi // channel: [ val(meta), rev-dwi, rev-bval, rev-bvec ], optional
ch_rev_b0 // channel: [ val(meta), rev-b0 ], optional
ch_config_topup // channel: [ 'topup.cnf' ], optional

main:
ch_versions = Channel.empty()

// ** Create channel for TOPUP ** //
// Input : [ meta, dwi, bval, bvec, b0 | [], rev-dwi | [], rev-bval | [], rev-bvec | [], rev-b0 | [] ]
// - join [ meta, dwi, bval, bvec, b0 | null ]
// - map [ meta, dwi, bval, bvec, b0 | [] ]
// - join [ meta, dwi, bval, bvec, b0 | [] ] + [ rev-dwi, rev-bval, rev-bvec ] | [ null ]
// - map [ meta, dwi, bval, bvec, b0 | [], rev-dwi | [], rev-bval | [], rev-bvec | [] ]
// - join [ meta, dwi, bval, bvec, b0 | [], rev-dwi | [], rev-bval | [], rev-bvec | [], rev-b0 | null ]
// - map [ meta, dwi, bval, bvec, b0 | [], rev-dwi | [], rev-bval | [], rev-bvec | [], rev-b0 | [] ]
// Result : [ meta, dwi, bval, bvec, b0 | [], rev-dwi | [], rev-bval | [], rev-bvec | [], rev-b0 | [] ]
// Steps :
// - join [ meta, dwi, bval, bvec, b0 | null ]
// - map [ meta, dwi, bval, bvec, b0 | [] ]
// - join [ meta, dwi, bval, bvec, b0 | [] ] + [ rev-dwi, rev-bval, rev-bvec ] | [ null ]
// - map [ meta, dwi, bval, bvec, b0 | [], rev-dwi | [], rev-bval | [], rev-bvec | [] ]
// - join [ meta, dwi, bval, bvec, b0 | [], rev-dwi | [], rev-bval | [], rev-bvec | [], rev-b0 | null ]
// - map [ meta, dwi, bval, bvec, b0 | [], rev-dwi | [], rev-bval | [], rev-bvec | [], rev-b0 | [] ]
//
// Final filter ensures DWI comes with either a rev-dwi (index 5) or a rev-b0 (index 8)
// Finally, to create ch_topup, filter ensures DWI comes with either a rev-dwi (index 5) or a rev-b0 (index 8)
ch_topup = ch_dwi
.join(ch_b0, remainder: true)
.map{ it[0..3] + [it[4] ?: []] }
Expand All @@ -42,15 +43,16 @@ workflow TOPUP_EDDY {
ch_versions = ch_versions.mix(PREPROC_TOPUP.out.versions.first())

// ** Create channel for EDDY ** //
// Input : [ meta, dwi, bval, bvec, rev-dwi | [], rev-bval | [], rev-bvec | [], b0 | [], coeffs | [], movpar | [] ]
// - join [ meta, dwi, bval, bvec ] + [ rev-dwi, rev-bval, rev-bvec ] | [ null ]
// - map [ meta, dwi, bval, bvec, rev-dwi | [], rev-bval | [], rev-bvec | [] ]
// - join [ meta, dwi, bval, bvec, rev-dwi | [], rev-bval | [], rev-bvec | [], b0 | null ]
// - map [ meta, dwi, bval, bvec, rev-dwi | [], rev-bval | [], rev-bvec | [], b0 | [] ]
// - join [ meta, dwi, bval, bvec, rev-dwi | [], rev-bval | [], rev-bvec | [], b0 | [], coeffs | null ]
// - map [ meta, dwi, bval, bvec, rev-dwi | [], rev-bval | [], rev-bvec | [], b0 | [], coeffs | [] ]
// - join [ meta, dwi, bval, bvec, rev-dwi | [], rev-bval | [], rev-bvec | [], b0 | [], coeffs | [], movpar | null ]
// - map [ meta, dwi, bval, bvec, rev-dwi | [], rev-bval | [], rev-bvec | [], b0 | [], coeffs | [], movpar | [] ]
// Result : [ meta, dwi, bval, bvec, rev-dwi | [], rev-bval | [], rev-bvec | [], b0 | [], coeffs | [], movpar | [] ]
// Steps :
// - join [ meta, dwi, bval, bvec ] + [ rev-dwi, rev-bval, rev-bvec ] | [ null ]
// - map [ meta, dwi, bval, bvec, rev-dwi | [], rev-bval | [], rev-bvec | [] ]
// - join [ meta, dwi, bval, bvec, rev-dwi | [], rev-bval | [], rev-bvec | [], b0 | null ]
// - map [ meta, dwi, bval, bvec, rev-dwi | [], rev-bval | [], rev-bvec | [], b0 | [] ]
// - join [ meta, dwi, bval, bvec, rev-dwi | [], rev-bval | [], rev-bvec | [], b0 | [], coeffs | null ]
// - map [ meta, dwi, bval, bvec, rev-dwi | [], rev-bval | [], rev-bvec | [], b0 | [], coeffs | [] ]
// - join [ meta, dwi, bval, bvec, rev-dwi | [], rev-bval | [], rev-bvec | [], b0 | [], coeffs | [], movpar | null ]
// - map [ meta, dwi, bval, bvec, rev-dwi | [], rev-bval | [], rev-bvec | [], b0 | [], coeffs | [], movpar | [] ]
ch_eddy_input = ch_dwi
.join(ch_rev_dwi, remainder: true)
.map{ it[0..3] + [it[4] ? it[4..-1] : [], [], []] }
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