Home

Documentation

GitHub

Anat_mni_tpms pipeline

Get templates tissues probability map and register them in subject space

  • Get white matter (WM), grey matter (GM) and cerebrospinal (CSF) from ‘MNI152NLin2009cAsym’ template (resolution 1 mm).

  • Adapted from mriqc anatomical workflow.

Pipeline insight

Anat_mni_tpms pipeline combines the following pipelines and processes:
- Get tissue map templates (CSF, GM and WM) from templateFlow
(default values : in_template = ‘MNI152NLin2009cAsym’, resolution = 1, suffix = ‘probseg’, label = ‘CSF’ or ‘GM’ or ‘WM’)
- Apply Transform
(default values: interpolation = ‘Linear’)
Anat MNI templates pipeline

Mandatory inputs parameters

  • inverse_composite_transform (a string representing an existing file)

    Inverse composite transform used in “ApplyTransform” process (MNI space –> ‘in_ras’ space).

    ex. '/home/username/data/raw_data/T1w_masked_InverseComposite.h5'
  • in_ras (a string representing an existing file)

    An anatomical image (T1w or T2w) (valid extensions: [.nii, .nii.gz]).

    ex. '/home/username/data/raw_data/T1w.nii'

Outputs parameters:

  • mni_tpms (a list representing files)

    Air mask.

    ex. ['/home/username/data/derived_data/csf_tpl-MNI152NLin2009cAsym_res-01_label-CSF_probseg.nii', '/home/username/data/derived_data/gm_tpl-MNI152NLin2009cAsym_res-01_label-GM_probseg.nii', '/home/username/data/derived_data/wm_tpl-MNI152NLin2009cAsym_res-01_label-WM_probseg.nii']

Useful links:

mriqc v22.06