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[ENH] Update subworkflow preproc_t1 #35

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[ENH] Update subworkflow preproc_t1 #35

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3877194
update main
anroy1 Oct 29, 2024
dcd9d29
Remove remainder to antsbet inputs
anroy1 Nov 1, 2024
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40 changes: 29 additions & 11 deletions subworkflows/nf-neuro/preproc_t1/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -25,23 +25,37 @@ workflow PREPROC_T1 {
ch_versions = Channel.empty()

// ** Denoising ** //
ch_nlmeans = ch_image.join(ch_mask_nlmeans)
ch_nlmeans = ch_image
.join(ch_mask_nlmeans, remainder: true)
.map{ it[0..1] + [it[2] ?: []] }

DENOISING_NLMEANS ( ch_nlmeans )
ch_versions = ch_versions.mix(DENOISING_NLMEANS.out.versions.first())

// ** N4 correction ** //
ch_N4 = DENOISING_NLMEANS.out.image.join(ch_ref_n4)
ch_N4 = DENOISING_NLMEANS.out.image
.join(ch_ref_n4, remainder: true)
.map{ it[0..1] + [it[2] ?: []] }
.join(ch_mask_nlmeans, remainder: true)
.map{ it[0..2] + [it[3] ?: []] }

PREPROC_N4 ( ch_N4 )
ch_versions = ch_versions.mix(PREPROC_N4.out.versions.first())

// ** Resampling ** //
ch_resampling = PREPROC_N4.out.image.join(ch_ref_resample)
ch_resampling = PREPROC_N4.out.image
.join(ch_ref_resample, remainder: true)
.map{ it[0..1] + [it[2] ?: []] }

IMAGE_RESAMPLE ( ch_resampling )
ch_versions = ch_versions.mix(IMAGE_RESAMPLE.out.versions.first())

// ** Brain extraction ** //
if ( params.run_synthbet) {
ch_bet = IMAGE_RESAMPLE.out.image.join(ch_weights)
ch_bet = IMAGE_RESAMPLE.out.image
.join(ch_weights, remainder: true)
.map{ it[0..1] + [it[2] ?: []] }

BETCROP_SYNTHBET ( ch_bet )
ch_versions = ch_versions.mix(BETCROP_SYNTHBET.out.versions.first())

Expand All @@ -51,9 +65,10 @@ workflow PREPROC_T1 {
}

else {
ch_template = ch_template.ifEmpty(Channel.error('Template is required for ANTS registration'))
ch_probability_map = ch_probability_map.ifEmpty(Channel.error('Probability map is required for ANTS registration'))
ch_bet = IMAGE_RESAMPLE.out.image.join(ch_template).join(ch_probability_map)
ch_bet = IMAGE_RESAMPLE.out.image
.join(ch_template)
.join(ch_probability_map)

BETCROP_ANTSBET ( ch_bet )
ch_versions = ch_versions.mix(BETCROP_ANTSBET.out.versions.first())

Expand All @@ -62,13 +77,16 @@ workflow PREPROC_T1 {
mask_bet = BETCROP_ANTSBET.out.mask
}

// ** crop image ** //
ch_crop = image_bet.map{it + [[]]}
// ** Crop image ** //
ch_crop = image_bet
.map{ it + [[]] }

BETCROP_CROPVOLUME_T1 ( ch_crop )
ch_versions = ch_versions.mix(BETCROP_CROPVOLUME_T1.out.versions.first())

// ** crop mask ** //
ch_crop_mask = mask_bet.join(BETCROP_CROPVOLUME_T1.out.bounding_box)
// ** Crop mask ** //
ch_crop_mask = mask_bet
.join(BETCROP_CROPVOLUME_T1.out.bounding_box)

BETCROP_CROPVOLUME_MASK ( ch_crop_mask )
ch_versions = ch_versions.mix(BETCROP_CROPVOLUME_MASK.out.versions.first())
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