Conversion of clinical data

[fyb99]

Hi, recently I am using clinica to convert the ADNI and AIBL datasets. After converting them, I find the tsv files that are used to store clinica data only contain limited columns. How could I modify the default settings and convert all the clinica data in the dataset?

[NicolasGensollen]

Hi @fyb99

Could you be a bit more specific ? Which TSV files exactly are you talking about ? What are the columns you were expecting ?

Thanks
Best

[fyb99]

Hi, for example, when I convert the clinica data for AIBL dataset, the obtained files are shown as below (paticipants.tsv and sessions.tsv). When I check the original clinica data, I find it indeed have much more attributes (i.e., columns in the table). During the converting, I guess the clinica only convert the essencial clinica which maybe are pre-defined in the code. How I can convert all the clinical data, where should I modify?

[NicolasGensollen]

Hi @fyb99

Clinica defines the clinical data which should be converted for each converter and for each file (participants.tsv, sessions.tsv, and scans.tsv). There are basic mappings that were done for each file and each converter which map the BIDS name to the name in the raw data as well as where to find it. For AIBL, these files are in clinica.iotools.converters.specifications. For example:

https://github.com/aramis-lab/clinica/blob/dev/clinica/iotools/converters/specifications/participant.tsv

In the code, the function using these specifications to write the participants.tsv file of AIBL is here:

clinica/clinica/iotools/converters/aibl_to_bids/utils/clinical.py

Lines 14 to 19 in 1886a29

	def create_participants_tsv_file(
	input_path: Path,
	clinical_specifications_folder: Path,
	clinical_data_dir: Path,
	delete_non_bids_info: bool = True,
	) -> None:

If some data are not converted, you might want to add them to the specification files.

Hope this is helping a bit !

[fyb99]

Sorry for the late reply. I have check the python file. It clearly shows the converted dataframe and the used csv files. I am a little bit confused how to update the specifiction file if I want to converts some attributes from other clinical tables, such as the aibl_medhist_01-Jun-2018.csv. Do you mean what I should do is to add my desired attributes in the tsv file without modifying any code? What template should the addition step follow?

[AliceJoubert]

Hello @fyb99, do you have an idea as to which tsv you want to modify and for what purpose (ex : getting info for one specific subject or for a specific subject at a specific session ?) ? Also, which version of clinica are you using ?