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

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

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