Skip to content

check-missing-modalities - Check missing modalities for each subject

Deprecation

This iotool will soon (next release) not be supported by clinica anymore. The new python library clinicaio will take on this functionality.

Starting from a BIDS compliant dataset, this command creates:

  1. <prefix>_ses-<session_label>.tsv: TSV files for each session available with the list of the modalities found for each subject.
  2. <prefix>_summary.txt: a text file containing the number and the percentage of modalities missing for each session.
  3. analysis.txt: a text file in which a table is written per session. This table contains the number of images per modality per diagnosis when the column diagnosis is available in the session-level files of the BIDS directory.

If no value for <prefix> is specified by the user, the default will be missing_mods.

clinica iotools check-missing-modalities [OPTIONS] BIDS_DIRECTORY OUTPUT_DIRECTORY

where:

  • BIDS_DIRECTORY: input folder of a BIDS compliant dataset
  • OUTPUT_DIRECTORY: output folder
  • -op / --output_prefix (Optional): prefix used for the name of the output files.

If not specified the default value will be missing_mods

If, for example, only the session M00 is available and the parameter -op is not specified, the command will create the files:

  • missing_mods_ses-M000.tsv
  • missing_mods_summary.txt.

The content of missing_mods_ses-M000.tsv will look like:

participant_id   T1w   DWI
sub-01           1       1
sub-02           1       0
sub-03           1       0

Where the column participant_id contains all the subjects found and the following columns correspond to the list of all the modalities available for the given dataset. The availability is expressed by a boolean value.

The nomenclature of the modalities tries to follow, as much as possible, the one proposed by the BIDS standard.

Example

clinica iotools check-missing-modalities /Home/ADNI_BIDS/ /Home/
clinica iotools check-missing-modalities /Home/ADNI_BIDS/ /Home/ -op new_name

Contact us !