USAGE

SCIL ihMT pipeline
==================

Pipeline for myelin indices maps from the Magnetization Transfer
(MT) and inhomogeneous Magnetization Transfer (ihMT).
Resulting maps could be corrected or not for an empiric B1 correction maps.

OUTPUT STRUCTURE

Root output folder
    [root]
    ├── S1 (One folder per subject)
    │   ├── Register_ihMT_maps - ihMT and MT ratio and saturation maps in diffusion space
    │   ├── Register_contrast_maps - The 5 contrast images in diffusion space
    │   ├── Register_MT_T1w - The MT T1w in diffusion space: Used as reference for MT and ihMT saturation image processing
    │   ├── Contrasts_ihMT_maps (option extended) - The 5 contrast images and the MT T1w reference image in native space
    │   ├── ihMT_native_maps (option extended) - ihMT and MT ratio and saturation maps in native space
    │   ├── Segmentation (option extended) - Segmentation maps resulting from antsAtropos
    │   ├── Coregistered_images (option extended) - Coregistration of all images (echoes) on the reference image (echo-1_acq-pos_ihmt)
    │   ├── Bet_images (option extended) - All coregister images after brain extraction and brain mask
    │   └── Registration_files (option extended) - Transformation files resulting from ihMT image registration in diffusion space
    ├── S2
    │   ├── Register_ihMT_maps


USAGE

nextflow run main.nf [optional_args] (--input)

DESCRIPTION

--input=/path/to/[root]     Root folder contaning one or multiple subject(s)
                            [root]
                            ├── S1
                            │   ├── *echo-*_acq-altpn_ihmt.nii.gz/.json
                            │   ├── *echo-*_acq-altnp_ihmt.nii.gz/.json
                            │   ├── *echo-*_acq-mtoff_ihmt.nii.gz/.json
                            │   ├── *echo-*_acq-neg_ihmt.nii.gz/.json
                            │   ├── *echo-*_acq-pos_ihmt.nii.gz/.json
                            │   ├── *echo-*_acq-T1w_ihmt.nii.gz/.json
                            │   ├── ref.nii.gz (This is a copy of echo-1_acq-pos_ihmt)
                            │   ├── t1_brain_on_b0.nii.gz
                            │   ├── *b1.nii.gz (optional)
                            └── S2
                                ├── *echo-*_acq-altpn_ihmt.nii.gz/.json
                                ├── *echo-*_acq-altnp_ihmt.nii.gz/.json
                                ├── *echo-*_acq-mtoff_ihmt.nii.gz/.json
                                ├── *echo-*_acq-neg_ihmt.nii.gz/.json
                                ├── *echo-*_acq-pos_ihmt.nii.gz/.json
                                ├── *echo-*_acq-T1w_ihmt.nii.gz/.json
                                ├── ref.nii.gz (This is a copy of echo-1_acq-pos_ihmt)
                                ├── t1_brain_on_b0.nii.gz
                                └── *b1.nii.gz (optional)


Files should come out of the Tractoflow pipeline, with the following source:
- t1_brain_on_b0.nii.gz: from Register_T1


OPTIONAL ARGUMENTS (default value)

--ihmt_num_threads            Number of threads to use for ihmt ($ihmt_num_threads)
--bet_T1w                     Fractional Intensity threshold for BET on T1weighted ihmt image ($bet_T1w).
--filtering                   If set, it will apply Gaussian filtering to remove Gibbs ringing ($filtering).
--extended                    If set, ihMT_flow will output multiple complementary data ($extended).