diff --git a/CHANGELOG.md b/CHANGELOG.md index 72bfe99..9145f5a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,5 +7,5 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` -* Complete test suites for the pipeline using stub-runs. -* Complete port of [Infant-DWI](https://github.com/scilus/Infant-DWI/) modules and workflows into the nf-core template. +- Complete test suites for the pipeline using stub-runs. +- Complete port of [Infant-DWI](https://github.com/scilus/Infant-DWI/) modules and workflows into the nf-core template. diff --git a/docs/output.md b/docs/output.md index 14d1acd..ae13166 100644 --- a/docs/output.md +++ b/docs/output.md @@ -134,6 +134,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and data proces Output files - `dwi/` + - `*_space-diff_desc-filtered_tracking.{trk,h5}`: Filtered whole-brain tractogram. - `*_space-orig_desc-preproc_tracking.h5`: Final preprocessed decomposed whole-brain tractogram. - `*.npy`: Connectivity matrices for all supplied metrics. @@ -145,6 +146,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and data proces ### FreeSurfer +
Output files diff --git a/docs/usage.md b/docs/usage.md index 389b728..30335cc 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -6,10 +6,10 @@ `nf-pediatric` process MRI pediatric data from 0-18 years old. It includes a variety of profiles that performs different steps of the pipeline and can be activated or deactivated by the user. A specific and unique profile pertains to `infant` data (<2 years old) and sets specific parameters tailored to infant data preprocessing. Here is a list of the available profiles: -* `tracking`: Perform DWI preprocessing, DTI and FODF modelling, anatomical segmentation, and tractography. Final outputs are the DTI/FODF metric maps, whole-brain tractogram, registered anatomical image, etc. -* `freesurfer`: Run FreeSurfer or FastSurfer for T1w surface reconstruction. Then, the [Brainnetome Child Atlas](https://academic.oup.com/cercor/article/33/9/5264/6762896) is mapped to the subject space. **Not available with the `infant` profile.** -* `connectomics`: Perform tractogram segmentation according to an atlas, tractogram filtering, and compute metrics. Final outputs are connectivity matrices. -* `infant`: This profile adapt some processing steps to infant data, but also requires more input files. See below for a list of the required files. +- `tracking`: Perform DWI preprocessing, DTI and FODF modelling, anatomical segmentation, and tractography. Final outputs are the DTI/FODF metric maps, whole-brain tractogram, registered anatomical image, etc. +- `freesurfer`: Run FreeSurfer or FastSurfer for T1w surface reconstruction. Then, the [Brainnetome Child Atlas](https://academic.oup.com/cercor/article/33/9/5264/6762896) is mapped to the subject space. **Not available with the `infant` profile.** +- `connectomics`: Perform tractogram segmentation according to an atlas, tractogram filtering, and compute metrics. Final outputs are connectivity matrices. +- `infant`: This profile adapt some processing steps to infant data, but also requires more input files. See below for a list of the required files. ## Samplesheet input for the `tracking` profile. @@ -44,80 +44,80 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p #### **`-profile freesurfer`** -| Column | Description | -| --------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| `subject` | Custom subject name. Spaces in sample names are automatically converted to underscores (`_`). | -| `t1` | Full path to the T1w file. File has to be in the nifti file format (`.nii` or `.nii.gz`). +| Column | Description | +| --------- | --------------------------------------------------------------------------------------------- | +| `subject` | Custom subject name. Spaces in sample names are automatically converted to underscores (`_`). | +| `t1` | Full path to the T1w file. File has to be in the nifti file format (`.nii` or `.nii.gz`). | #### **`-profile tracking,freesurfer`** or **`-profile tracking,freesurfer,connectomics`** -| Column | Description | -| --------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| `subject` | Custom subject name. Spaces in sample names are automatically converted to underscores (`_`). | -| `t1` | Full path to the T1w file. File has to be in the nifti file format (`.nii` or `.nii.gz`). -| `dwi` | Full path to the DWI file. File has to be in the nifti file format (`.nii` or `.nii.gz`). -| `bval` | Full path to the file containing the b-values. -| `bvec` | Full path to the file containing the b-vectors. -| `rev_b0` | Full path to the reverse-phase encoded DWI file. File has to be in the nifti file format (`.nii` or `.nii.gz`). -| `metrics` | Full path to the **folder** containing additional metrics. Files within this folder has to be in the nifti file format (`.nii` or `.nii.gz`). **Optional, can only be supplied if `-profile connectomics` is selected.** +| Column | Description | +| --------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | +| `subject` | Custom subject name. Spaces in sample names are automatically converted to underscores (`_`). | +| `t1` | Full path to the T1w file. File has to be in the nifti file format (`.nii` or `.nii.gz`). | +| `dwi` | Full path to the DWI file. File has to be in the nifti file format (`.nii` or `.nii.gz`). | +| `bval` | Full path to the file containing the b-values. | +| `bvec` | Full path to the file containing the b-vectors. | +| `rev_b0` | Full path to the reverse-phase encoded DWI file. File has to be in the nifti file format (`.nii` or `.nii.gz`). | +| `metrics` | Full path to the **folder** containing additional metrics. Files within this folder has to be in the nifti file format (`.nii` or `.nii.gz`). **Optional, can only be supplied if `-profile connectomics` is selected.** | #### **`-profile connectomics,freesurfer`** -| Column | Description | -| --------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| `subject` | Custom subject name. Spaces in sample names are automatically converted to underscores (`_`). | -| `t1` | Full path to the T1w file. File has to be in the nifti file format (`.nii` or `.nii.gz`). -| `dwi` | Full path to the DWI file. File has to be in the nifti file format (`.nii` or `.nii.gz`). -| `bval` | Full path to the file containing the b-values. -| `bvec` | Full path to the file containing the b-vectors. -| `trk` | Full path to the whole-brain tractogram. File has to be in the `.trk` file format. -| `peaks` | Full path to the file containing the fODF peaks. File has to be in the nifti file format (`.nii` or `.nii.gz`). -| `fodf` | Full path to the fODF file. File has to be in the nifti file format (`.nii` or `.nii.gz`). -| `mat` | Full path to the affine transform required to register your anatomical image to the diffusion space. -| `warp` | Full path to the warp transform required to register your anatomical image to the diffusion space. -| `metrics` | Full path to the **folder** containing additional metrics. Files within this folder has to be in the nifti file format (`.nii` or `.nii.gz`). **Optional** +| Column | Description | +| --------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------- | +| `subject` | Custom subject name. Spaces in sample names are automatically converted to underscores (`_`). | +| `t1` | Full path to the T1w file. File has to be in the nifti file format (`.nii` or `.nii.gz`). | +| `dwi` | Full path to the DWI file. File has to be in the nifti file format (`.nii` or `.nii.gz`). | +| `bval` | Full path to the file containing the b-values. | +| `bvec` | Full path to the file containing the b-vectors. | +| `trk` | Full path to the whole-brain tractogram. File has to be in the `.trk` file format. | +| `peaks` | Full path to the file containing the fODF peaks. File has to be in the nifti file format (`.nii` or `.nii.gz`). | +| `fodf` | Full path to the fODF file. File has to be in the nifti file format (`.nii` or `.nii.gz`). | +| `mat` | Full path to the affine transform required to register your anatomical image to the diffusion space. | +| `warp`  | Full path to the warp transform required to register your anatomical image to the diffusion space. | +| `metrics` | Full path to the **folder** containing additional metrics. Files within this folder has to be in the nifti file format (`.nii` or `.nii.gz`). **Optional** | #### **`-profile connectomics`** or **`-profile connectomics,infant`** -| Column | Description | -| --------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| `subject` | Custom subject name. Spaces in sample names are automatically converted to underscores (`_`). | -| `t1` or `t2` | Full path to the T1w/T2w file. File has to be in the nifti file format (`.nii` or `.nii.gz`). -| `dwi` | Full path to the DWI file. File has to be in the nifti file format (`.nii` or `.nii.gz`). -| `bval` | Full path to the file containing the b-values. -| `bvec` | Full path to the file containing the b-vectors. -| `labels` | Full path to the file containing your labels to use in the segmentation. File has to be in the nifti file format (`.nii` or `.nii.gz`). -| `trk` | Full path to the whole-brain tractogram. File has to be in the `.trk` file format. -| `peaks` | Full path to the file containing the fODF peaks. File has to be in the nifti file format (`.nii` or `.nii.gz`). -| `fodf` | Full path to the fODF file. File has to be in the nifti file format (`.nii` or `.nii.gz`). -| `mat` | Full path to the affine transform required to register your anatomical image to the diffusion space. -| `warp` | Full path to the warp transform required to register your anatomical image to the diffusion space. -| `metrics` | Full path to the **folder** containing additional metrics. Files within this folder has to be in the nifti file format (`.nii` or `.nii.gz`). **Optional** +| Column | Description | +| ------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------- | +| `subject` | Custom subject name. Spaces in sample names are automatically converted to underscores (`_`). | +| `t1` or `t2` | Full path to the T1w/T2w file. File has to be in the nifti file format (`.nii` or `.nii.gz`). | +| `dwi` | Full path to the DWI file. File has to be in the nifti file format (`.nii` or `.nii.gz`). | +| `bval` | Full path to the file containing the b-values. | +| `bvec` | Full path to the file containing the b-vectors. | +| `labels` | Full path to the file containing your labels to use in the segmentation. File has to be in the nifti file format (`.nii` or `.nii.gz`). | +| `trk` | Full path to the whole-brain tractogram. File has to be in the `.trk` file format. | +| `peaks` | Full path to the file containing the fODF peaks. File has to be in the nifti file format (`.nii` or `.nii.gz`). | +| `fodf` | Full path to the fODF file. File has to be in the nifti file format (`.nii` or `.nii.gz`). | +| `mat` | Full path to the affine transform required to register your anatomical image to the diffusion space. | +| `warp`  | Full path to the warp transform required to register your anatomical image to the diffusion space. | +| `metrics` | Full path to the **folder** containing additional metrics. Files within this folder has to be in the nifti file format (`.nii` or `.nii.gz`). **Optional** | #### **`-profile tracking,infant`** -| Column | Description | -| --------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| `subject` | Custom subject name. Spaces in sample names are automatically converted to underscores (`_`). | -| `t2` | Full path to the T2w file. File has to be in the nifti file format (`.nii` or `.nii.gz`). -| `dwi` | Full path to the DWI file. File has to be in the nifti file format (`.nii` or `.nii.gz`). -| `bval` | Full path to the file containing the b-values. -| `bvec` | Full path to the file containing the b-vectors. -| `rev_b0` | Full path to the reverse-phase encoded DWI file. File has to be in the nifti file format (`.nii` or `.nii.gz`). -| `wmparc` | Full path to the WM mask file. File has to be in the nifti file format (`.nii` or `.nii.gz`). +| Column | Description | +| --------- | --------------------------------------------------------------------------------------------------------------- | +| `subject` | Custom subject name. Spaces in sample names are automatically converted to underscores (`_`). | +| `t2` | Full path to the T2w file. File has to be in the nifti file format (`.nii` or `.nii.gz`). | +| `dwi` | Full path to the DWI file. File has to be in the nifti file format (`.nii` or `.nii.gz`). | +| `bval` | Full path to the file containing the b-values. | +| `bvec` | Full path to the file containing the b-vectors. | +| `rev_b0` | Full path to the reverse-phase encoded DWI file. File has to be in the nifti file format (`.nii` or `.nii.gz`). | +| `wmparc` | Full path to the WM mask file. File has to be in the nifti file format (`.nii` or `.nii.gz`). | #### **`-profile tracking,connectomics,infant`** -| Column | Description | -| --------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| `subject` | Custom subject name. Spaces in sample names are automatically converted to underscores (`_`). | -| `t2` | Full path to the T2w file. File has to be in the nifti file format (`.nii` or `.nii.gz`). -| `dwi` | Full path to the DWI file. File has to be in the nifti file format (`.nii` or `.nii.gz`). -| `bval` | Full path to the file containing the b-values. -| `bvec` | Full path to the file containing the b-vectors. -| `rev_b0` | Full path to the reverse-phase encoded DWI file. File has to be in the nifti file format (`.nii` or `.nii.gz`). -| `labels` | Full path to the file containing your labels to use in the segmentation. File has to be in the nifti file format (`.nii` or `.nii.gz`). -| `wmparc` | Full path to the WM mask file. File has to be in the nifti file format (`.nii` or `.nii.gz`). +| Column | Description | +| --------- | --------------------------------------------------------------------------------------------------------------------------------------- | +| `subject` | Custom subject name. Spaces in sample names are automatically converted to underscores (`_`). | +| `t2` | Full path to the T2w file. File has to be in the nifti file format (`.nii` or `.nii.gz`). | +| `dwi` | Full path to the DWI file. File has to be in the nifti file format (`.nii` or `.nii.gz`). | +| `bval` | Full path to the file containing the b-values. | +| `bvec` | Full path to the file containing the b-vectors. | +| `rev_b0` | Full path to the reverse-phase encoded DWI file. File has to be in the nifti file format (`.nii` or `.nii.gz`). | +| `labels` | Full path to the file containing your labels to use in the segmentation. File has to be in the nifti file format (`.nii` or `.nii.gz`). | +| `wmparc` | Full path to the WM mask file. File has to be in the nifti file format (`.nii` or `.nii.gz`). | ## Running the pipeline