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

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Inputs

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

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

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Outputs

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

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

Format : path(versions.yml)

	Type	Description	Mandatory	Pattern
versions.yml	file	File containing software versions	True	versions.yml

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Arguments (see process.ext)

	Type	Description	Default	Choices
single_thread	boolean	If true, the command will be run in single-threaded mode. By default, the command will use multiple threads based on the number of CPUs allocated to the task.	False

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Tools

	Description	DOI
scilpy	The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox.

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Authors

• @karanphil

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Last updated : 2026-05-12