reconst_ihmt
Compute myelin indices maps from the MT and ihMT images. Please refer to https://github.com/scilus/scilpy/blob/2ced08f4d70cef1d7e4b089872f7593bf5b2833a/scripts/scil_mti_maps_ihMT.py to understand input format.
Keywords : magnetization transfer imaging, inhomogeneous magnetization transfer, myelin
Inputs
Section titled “Inputs”Input 1
Section titled “Input 1”Format : tuple val(meta), val(altpn), val(altnp), val(pos), val(neg), val(mtoff_pd)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| altpn | list | List of files (path to all echoes) corresponding to the alternation of positive and negative frequency saturation pulse. | True | *atlpn*.{nii,nii.gz} |
| altnp | list | List of files (path to all echoes) corresponding to the alternation of negative and positive frequency saturation pulse. | True | *altnp*.{nii,nii.gz} |
| pos | list | List of files (path to all echoes) corresponding to the positive frequency saturation pulse. | True | *pos*.{nii,nii.gz} |
| neg | list | List of files (path to all echoes) corresponding to the negative frequency saturation pulse. | True | *neg*.{nii,nii.gz} |
| mtoff_pd | list | List of files (path to all echoes) corresponding to the predominant PD (proton density) weighting images with no saturation pulse. | True | *mtoff_pd*.{nii,nii.gz} |
Input 2
Section titled “Input 2”Format : tuple val(mtoff_t1), path(mask), val(jsons), val(acq_params), path(b1), val(b1_fit)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| mtoff_t1 | list | List of files (path to all echoes) corresponding to the predominant T1 weighting images with no saturation pulse. | True | *mtoff_t1*.{nii,nii.gz} |
| mask | file | Nifti brain mask. | True | *mask.{nii,nii.gz} |
| jsons | list | List of json files for acquisition parameters extraction in the case of a Philips acquisition, otherwise use acq_params. Should be a json file for the mtoff_pd and mtoff_t1 files, in that order. | True | *.json |
| acq_params | list | List of values for acquisition parameters extraction. Should be in that order; flip angle of mtoff_pd, flip angle of mtoff_t1, TR of mtoff_pd, TR of mtoff_t1 (where TR = repetition time). | True | |
| b1 | file | Nifti file containing a coregistered B1 map. | True | *b1*.{nii,nii.gz} |
| b1_fit | list | List of files for the model based B1 correction method. | True | *fitValues*.mat |
Outputs
Section titled “Outputs”ihmt_maps
Section titled “ihmt_maps”Format : tuple val(meta), path(ihMT_native_maps)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| ihMT_native_maps | directory | Folder containing ihMT maps in native space. (MTR and ihMTR, plus MTsat and ihMTsat if mtoff_t1 was given) | True | ihMT_native_maps |
comp_maps
Section titled “comp_maps”Format : tuple val(meta), path(Complementary_maps)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| Complementary_maps | directory | Folder containing complementary maps. (intermediate files, B1 correction files, if extended option given) | True | Complementary_maps |
versions
Section titled “versions”Format : path(versions.yml)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| versions.yml | file | File containing software versions | True | versions.yml |
| Description | DOI | |
|---|---|---|
| scilpy | The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox. |
Authors
Section titled “Authors”Last updated : 2025-10-30