Could not run `clinica convert`
First of all, thank you for you work! I hope this repo will really help a lot to work with images.
However, I have some problems with running clinica.
This is what I want:
- I want to convert ADNI images to BIDS format (using
clinica convert adni-to-bids) and process them afterwards.
- Since ADNI database is extremely huge, I want to convert only T1 modality for specific subset of subjects.
What I do:
- I download all clinical data from ADNI.LONI.USC.EDU
- Download several images (MRPAGE, 2 subjects).
- Create 3 folders:
- "clinical_data" with all .csv
- "image_data" with 2 subfolders corresponding to subject id
- "bids_directory" - empty
- Create subject list "subjects.txt"
- Run the next command
clinica convert adni-to-bids -sl subjects.txt image_data/ clinical_data/ bids_directory/ --modatilities T1
- Below is error I receive: there is no file "IDA_MR_Metadata_Listing.csv"
Could you, please, help me tackle this problem or simply share the missing file "IDA_MR_Metadata_Listing.csv". It also would be great if you write in more details the documentation how to convert adni dataset to bids format and convert and afterwards.
Thank you! Wish you luck!
Hello Yaroslav! Thank you for using Clinica and for reporting the issue.
The problem is caused by changes in ADNI database. Csv files available for download at ida.loni.usc.edu have changed and in the latest version "IDA_MR_Metadata_Listing.csv" is not present anymore.
We are working on the code in order to make it usable again as soon as possible.
Thanks again, Simona