PreparingYourData

How to prepare your data?

In order to use Clinica pipelines by command line, you will need to give as input:

1. A dataset that follows the BIDS standard.
2. A file (named by default subject_sessions_list.tsv) with the list of all the available sessions for each subject.

This page explains how to obtain a BIDS compliant dataset and the file subject_sessions_list.tsv.

Dataset BIDS compliant

BIDS is a standard for organizing neuroimaging data and it has been also adopted by the Aramis team.

The pipelines used by command line work only if you give as input a BIDS compliant dataset. So, if your dataset doesn't follow this standard, you will need to convert to it.

On BIDS website is possible to find some tools that can help you for the conversion like, for example, the OpenfMRI to BIDS converter. A quick overwiev of the BIDS structure can be found on the BIDS page. For more details you can also check the documentation.

Note:

This is a future development and is still work in progress

Clinica offers the possibility to convert the ADNI dataset to BIDS standard using the following command:

clinica convert adni_to_bids dataset_directory output directory -c

Generate subject_sessions_list.tsv file

Together with a BIDS compliant dataset, you will need to give as input a TSV file with two columns (participant_id and session_id) containing the list of visits for each subject:

participant_id   session_id
sub-01           ses-M0
sub-01           ses-M24
sub-02           ses-M24

You can generate this file using Clinica with command create-subjects-visit:

clinica io create-subjects-visits bids_directory output_directory

More detail about the command can be found in the section Utilities in I/O page.