Module: 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.

Inputs

	Type	Description	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
altpn	list	List of files (path to all echoes) corresponding to the alternation of positive and negative frequency saturation pulse.	atlpn.{nii,nii.gz}
altnp	list	List of files (path to all echoes) corresponding to the alternation of negative and positive frequency saturation pulse.	altnp.{nii,nii.gz}
pos	list	List of files (path to all echoes) corresponding to the positive frequency saturation pulse.	pos.{nii,nii.gz}
neg	list	List of files (path to all echoes) corresponding to the negative frequency saturation pulse.	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.	mtoff_pd.{nii,nii.gz}
mtoff_t1	list	List of files (path to all echoes) corresponding to the predominant T1 weighting images with no saturation pulse.	mtoff_t1.{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.	*.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).
mask	file	Nifti brain mask.	*mask.{nii,nii.gz}
b1	file	Nifti file containing a coregistered B1 map.	b1.{nii,nii.gz}
b1_fit	list	List of files for the model based B1 correction method.	fitValues.mat

Outputs

	Type	Description	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
versions	file	File containing software versions	versions.yml
ihmt_maps	directory	Folder containing ihMT maps in native space. (MTR and ihMTR, plus MTsat and ihMTsat if mtoff_t1 was given)	ihMT_native_maps
comp_maps	directory	Folder containing complementary maps. (intermediate files, B1 correction files, if extended option given)	Complementary_maps

Tools

	Description	Homepage	DOI
Scilpy	The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox.	https://github.com/scilus/scilpy.git

Keywords

magnetization transfer imaging
inhomogeneous magnetization transfer
myelin

Authors

@karanphil