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.
| 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. | | 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 |
Authors
@karanphil
