IRTK Reconstruction

Fetal brain MRI reconstruction using IRTK reconstruction in a ChRIS ds plugin wrapper.

https://pubmed.ncbi.nlm.nih.gov/22939612/

Note

We recommend upgrading to NeSVoR

Usage

Quality assessment and inter-slice thickness should be defined by a .CSV file.

In the first column, the file name is specified. In the second column, the quality score (a float between 0-1) is given. In the third column, the inter-slice thickness in millimeters is given.

filename,quality,slice_thickness
a.nii,0.27163228,2.0
b.nii,0.7249744,2.0
c.nii,0.697088,2.0
d.nii,0.023986042,2.0
e.nii,0.849987,2.0

With this, the input to pl-irtk-reconstruction is tightly coupled to the output of pl-fetal-brain-assessment, v1.3.0. The default input options to pl-irtk-reconstruction are tailored to meet the default output names of pl-fetal-brain-assessment.

NOTE: the specific file path is not considered. Only the base name of the file names listed in the .CSV are relevant. These names are matched to files discovered by the option --inputPathFilter.

For an input tree like this:

in/
├── Best_Images_crop
│   ├── b.nii
│   ├── c.nii
│   └── e.nii
└── quality_assessment.csv

Command-line invocation:

singularity exec docker://fnndsc/pl-irtk-reconstruction:1.0.3 irtkrecon \
  --inputPathFilter 'Best_images_crop/*.nii' --csv 'quality_assessment.csv' \
  --output recon.nii --debug incoming/ outgoing/