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Merge pull request scilus#128 from Manonedde/preproc_dwi
[Subworkflow][WIP] Preprocessing DWI
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| Original file line number | Diff line number | Diff line change |
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| include { DENOISING_MPPCA as DENOISE_DWI } from '../../../modules/nf-scil/denoising/mppca/main' | ||
| include { DENOISING_MPPCA as DENOISE_REVDWI } from '../../../modules/nf-scil/denoising/mppca/main' | ||
| include { BETCROP_FSLBETCROP } from '../../../modules/nf-scil/betcrop/fslbetcrop/main' | ||
| include { BETCROP_CROPVOLUME } from '../../../modules/nf-scil/betcrop/cropvolume/main' | ||
| include { PREPROC_N4 as N4_DWI } from '../../../modules/nf-scil/preproc/n4/main' | ||
| include { PREPROC_NORMALIZE as NORMALIZE_DWI } from '../../../modules/nf-scil/preproc/normalize/main' | ||
| include { IMAGE_RESAMPLE as RESAMPLE_DWI } from '../../../modules/nf-scil/image/resample/main' | ||
| include { IMAGE_RESAMPLE as RESAMPLE_MASK } from '../../../modules/nf-scil/image/resample/main' | ||
| include { UTILS_EXTRACTB0 as EXTRACTB0_RESAMPLE } from '../../../modules/nf-scil/utils/extractb0/main' | ||
| include { UTILS_EXTRACTB0 as EXTRACTB0_TOPUP } from '../../../modules/nf-scil/utils/extractb0/main' | ||
| include { TOPUP_EDDY } from '../topup_eddy/main' | ||
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| workflow PREPROC_DWI { | ||
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| 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 | ||
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| main: | ||
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| ch_versions = Channel.empty() | ||
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| ch_denoise_dwi = ch_dwi | ||
| .multiMap { meta, dwi, bval, bvec -> | ||
| dwi: [ meta, dwi ] | ||
| bvs_files: [ meta, bval, bvec ] | ||
| } | ||
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| // ** Denoised DWI ** // | ||
| DENOISE_DWI ( ch_denoise_dwi.dwi ) | ||
| ch_versions = ch_versions.mix(DENOISE_DWI.out.versions.first()) | ||
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| if ( ch_rev_dwi ) | ||
| { | ||
| ch_denoise_rev_dwi = ch_rev_dwi | ||
| .multiMap { meta, dwi, bval, bvec -> | ||
| rev_dwi: [ [id: "${meta.id}_rev", cache: meta], dwi ] | ||
| rev_bvs_files: [ meta, bval, bvec ] | ||
| } | ||
| // ** Denoised reverse DWI ** // | ||
| DENOISE_REVDWI ( ch_denoise_rev_dwi.rev_dwi ) | ||
| ch_versions = ch_versions.mix(DENOISE_REVDWI.out.versions.first()) | ||
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| ch_topup_eddy_rev_dwi = DENOISE_REVDWI.out.image | ||
| .map{ meta, dwi -> [ meta.cache, dwi ] } | ||
| .join(ch_denoise_rev_dwi.rev_bvs_files) | ||
| } | ||
| else | ||
| { | ||
| ch_topup_eddy_rev_dwi = [] // or Channel.empty() | ||
| } | ||
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| // ** Eddy Topup ** // | ||
| ch_topup_eddy_dwi = DENOISE_DWI.out.image.join(ch_denoise_dwi.bvs_files) | ||
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| if ( ! ch_b0 ) { | ||
| EXTRACTB0_TOPUP { ch_topup_eddy_dwi } | ||
| ch_versions = ch_versions.mix(EXTRACTB0_TOPUP.out.versions.first()) | ||
| ch_b0 = EXTRACTB0_TOPUP.out.b0 | ||
| } | ||
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| 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()) | ||
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| // ** 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()) | ||
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| // ** 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()) | ||
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| // ** 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()) | ||
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| // ** Normalize DWI ** // | ||
| ch_normalize = N4_DWI.out.image | ||
| .join(BETCROP_FSLBETCROP.out.mask) | ||
| .join(TOPUP_EDDY.out.bval) | ||
| .join(TOPUP_EDDY.out.bvec) | ||
| NORMALIZE_DWI ( ch_normalize ) | ||
| ch_versions = ch_versions.mix(NORMALIZE_DWI.out.versions.first()) | ||
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| // ** Resample DWI ** // | ||
| ch_resample_dwi = NORMALIZE_DWI.out.dwi.map{ it + [[]] } | ||
| RESAMPLE_DWI ( ch_resample_dwi ) | ||
| ch_versions = ch_versions.mix(RESAMPLE_DWI.out.versions.first()) | ||
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| // ** Extract b0 ** // | ||
| ch_dwi_extract_b0 = RESAMPLE_DWI.out.image | ||
| .join(TOPUP_EDDY.out.bval) | ||
| .join(TOPUP_EDDY.out.bvec) | ||
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| EXTRACTB0_RESAMPLE { ch_dwi_extract_b0 } | ||
| ch_versions = ch_versions.mix(EXTRACTB0_RESAMPLE.out.versions.first()) | ||
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| // ** Resample mask ** // | ||
| ch_resample_mask = BETCROP_FSLBETCROP.out.mask.map{ it + [[]] } | ||
| RESAMPLE_MASK ( ch_resample_mask ) | ||
| ch_versions = ch_versions.mix(RESAMPLE_MASK.out.versions.first()) | ||
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| 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 ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,143 @@ | ||
| name: "preproc_dwi" | ||
| description: | | ||
| Subworkflow performing pre-processing of DWI image from from brain extraction to motion correction and resampling. | ||
| It requires at least one input channels including a DWI image with corresponding b-value (bval) and b-vector (bvec) files (ch_dwi). | ||
| The next 3 channels are optional and includes a reversed DWI image with correspond bval and bvec files (ch_rev_dwi), | ||
| a reversed phase encoded b = 0 image (ch_rev_b0) and a channel for Topup configuration file. | ||
| 1) Required channel include the following main steps: | ||
| Brain Extraction, Denoising, Eddy, N4 Bias Correction, Normalization, and Resampling. | ||
| 2) Required and optional channels include the following main steps: | ||
| Brain Extraction, Denoising, Topup+Eddy, N4 Bias Correction, Normalization and Resampling. | ||
| The resulting file from this subworkflows is a DWI that has been denoised, corrected for susceptibility, | ||
| eddy currents and motion, normalized, cropped and resampled. | ||
| The next step would be to extract diffusion profiles for the corrected DWI, using a module implementing either | ||
| DTI (see RECONST_DTI), fODF (see RECONST_FODF) or MAP-MRI (NotImplementedYet). | ||
| --------- Steps -------------------- | ||
| Brain Extraction (bet, FSL). | ||
| Extract brain mask from the b0 image and applied to the whole DWI. | ||
| This brain extraction is required to remove the skull and prepare the DWI to the T1 Registration. | ||
| Denoising (dwidenoise, MPPCA method, MRtrix3). | ||
| Used to remove the noise induced by the MRI acquisition, | ||
| enhance the signal to noise ratio and improve the image quality and following metrics. | ||
| The denoising is performed in the original spatial resolution and uses the MP-PCA method. | ||
| Topup (FSL - optional). | ||
| Topup uses the b=0 and reversed phase encoded b=0 images to extract the deformation field and | ||
| corrects the brain deformation induced by the magnetic field susceptibility artefacts. | ||
| Eddy (FSL). | ||
| Eddy corrects eddy-currents, motion artefacts and performs slice-wise outlier detection and correction. | ||
| When Topup is run, the eddy command is performed using the topup output. | ||
| N4 Bias Correction (N4BiasFieldCorrection, ANTs). | ||
| The N4 Bias Correction normalizes the image intensities and reduces this intensity bias | ||
| (the center of the brain is less intense than its outer boundary due to multi-channel | ||
| head coils). N4 correction is performed on the b=0 and applied to the whole DWI. | ||
| Normalize (dwinormalise, MRtrix3). | ||
| The DWI is normalized to have a mean value in the WM of approximately 1000. | ||
| This task permits analyzing datasets from different MRI scanners with the same acquisition scheme. | ||
| Resample (DIPY). | ||
| The DWI is resampled to 1 mm isotropic spatial resolution, which is usually the spatial | ||
| resolution of the T1. This spatial resolution is modifiable in the configuration file. | ||
| See Tractoflow for more details, https://www.sciencedirect.com/science/article/pii/S105381192030375X?via%3Dihub | ||
| keywords: | ||
| - Brain extraction | ||
| - Crop | ||
| - Denoising | ||
| - Topup-Eddy correction | ||
| - Normalization | ||
| - Resampling | ||
| components: | ||
| - betcrop/cropvolume | ||
| - betcrop/fslbetcrop | ||
| - denoising/mppca | ||
| - image/resample | ||
| - preproc/n4 | ||
| - preproc/normalize | ||
| - utils/extractb0 | ||
| - topup_eddy | ||
| input: | ||
| - ch_dwi: | ||
| type: file | ||
| description: | | ||
| The input channel containing the DWI file, B-values and B-vectors in FSL format files | ||
| Structure: [ val(meta), path(dwi), path(bval), path(bvec) ] | ||
| pattern: "*.{nii,nii.gz|bval|bvec}" | ||
| - ch_rev_dwi: | ||
| type: file | ||
| description: | | ||
| The input channel containing the reverse DWI file, reverse B-values and reverse B-vectors in FSL format files | ||
| Structure: [ val(meta), path(rev_dwi), path(bval), path(bvec) ] | ||
| pattern: "*.{nii,nii.gz|bval|bvec}" | ||
| - ch_b0: | ||
| type: file | ||
| description: | | ||
| The input channel containing the b0 file. This input is optional. | ||
| Structure: [ val(meta), path(rev_b0) ] | ||
| pattern: "*.{nii,nii.gz}" | ||
| - ch_rev_b0: | ||
| type: file | ||
| description: | | ||
| The input channel containing the reverse b0 file. This input is optional. | ||
| Structure: [ val(meta), path(rev_b0) ] | ||
| pattern: "*.{nii,nii.gz}" | ||
| - ch_config_topup: | ||
| type: file | ||
| description: | | ||
| The input channel containing the config file for Topup. This input is optional. See https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/TopupUsersGuide#Configuration_files | ||
| Structure: [ path(config_file) ] | ||
| pattern: "*.{cnf}" | ||
| output: | ||
| - dwi_resample: | ||
| type: file | ||
| description: | | ||
| Channel containing DWI denoised, corrected for susceptibility and/or eddy currents and motion, normalized, cropped and resampled. | ||
| Structure: [ val(meta), path(dwi) ] | ||
| pattern: "*_resampled.{nii,nii.gz}" | ||
| - bval: | ||
| type: file | ||
| description: | | ||
| Channel containing Eddy-corrected B-values in FSL format | ||
| Structure: [ val(meta), path(bval) ] | ||
| pattern: "*__bval_eddy" | ||
| - bvec: | ||
| type: file | ||
| description: | | ||
| Channel containing Eddy-corrected B-vectors in FSL format | ||
| Structure: [ val(meta), path(bvec) ] | ||
| pattern: "*__dwi_eddy_corrected.bvec" | ||
| - b0: | ||
| type: file | ||
| description: | | ||
| Channel containing b0 corrected file. | ||
| Structure: [ val(meta), path(b0) ] | ||
| pattern: "*__b0_bet.nii.gz" | ||
| - b0_mask: | ||
| type: file | ||
| description: | | ||
| Channel containing b0 corrected binary mask file. | ||
| Structure: [ val(meta), path(b0_mask) ] | ||
| pattern: "*__b0_bet_mask.nii.gz" | ||
| - dwi_bounding_box: | ||
| type: file | ||
| description: | | ||
| Channel containing the bounding box defining the limits of the crop. | ||
| Structure: [ val(meta), path(bounding_box) ] | ||
| pattern: "*.{pkl}" | ||
| - dwi_topup_eddy: | ||
| type: file | ||
| description: | | ||
| Channel containing DWI output after denoised, correction for susceptibility and/or eddy currents and motion (Topup-Eddy). | ||
| Structure: [ val(meta), path(dwi) ] | ||
| pattern: "*_corrected.{nii,nii.gz}" | ||
| - dwi_n4: | ||
| type: file | ||
| description: | | ||
| Channel containing DWI after denoised, corrected for susceptibility and/or eddy currents and motion, cropped and normalized (N4). | ||
| Structure: [ val(meta), path(dwi) ] | ||
| pattern: "*_normalized.{nii,nii.gz}" | ||
| - versions: | ||
| type: file | ||
| description: | | ||
| File containing software versions | ||
| Structure: [ path(versions.yml) ] | ||
| pattern: "versions.yml" | ||
| authors: | ||
| - "@medde" |
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