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ixi-to-bids – Conversion of Information eXtraction from Images (IXI) to BIDS format

Dataset Description

The Information eXtraction from Images is a project which issued a dataset of nearly 600 nifti images from healthy subjects. The MR acquisition protocol includes T1,T2, PD weighted, MRA and diffusion-weighted images. Three hospitals in London were involved in data collection.

Downloading the data

The IXI dataset can be downloaded freely from the IXI webpage.

Organising data with the aim of using the converter

The folders and files downloaded from the website should be left as they are (name, inner organisation...) but can be placed where the user wants them.

Using the converter

Available Modalities

DTI files are merged together to produce one DWI image.

The converter can convert to BIDS all the modalities offered by IXI : DTI ; T1 ; T2 ; PD ; angiography.

Dependencies

If you installed clinica, this converter needs no further dependencies.

Understanding the command line

clinica convert ixi-to-bids DATASET_DIRECTORY BIDS_DIRECTORY CLINICAL_DATA_DIRECTORY [OPTIONS]
where :

  • DATASET_DIRECTORY is the path to the raw IXI dataset directory, which should contain all the IXI folders previously downloaded :

    DATASET_DIRECTORY Organisation
    DATASET_DIRECTORY
├── IXI-T1
│   ├── IXI002-Guys-0828-T1.nii.gz
│   ├── ...
├── IXI-DTI
│   └── IXI002-Guys-0828-DTI-00.nii.gz
│   ├── ...
...

  • BIDS_DIRECTORY is the path to the BIDS folder to be created

  • CLINICAL_DATA_DIRECTORY is the path to the folder where the clinical data of the IXI dataset is stored.
    CLINICAL_DATA_DIRECTORY Organisation
        CLINICAL_DATA_DIRECTORY
    ├── IXI.xls
    ...

Optional parameters common to all converters

  • -- subjects_list / - sl : path to a text file containing a list of specific subjects to extract. The expected format is one subject per line :
  001_S_0001
  002_S_0002
  • -- n_procs / - np : Number of cores used to run in parallel. (default: (Number of available CPU minus one))

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