Once the data is in NIfTI format and has classifications (T1, T2star, etc.), we can use pre-curation to rename the scans across the entire project quickly and easily.
This step is optional. You do not need to run pre-curation if:
- You have ReproIn-compliant names from the scanner OR
- You have chosen to alter the curation Gear templates. Note that altering the templates is considerably more difficult than running pre-curation.
- Step 1: Review the README for the pre-curation gear
- Step 2: Run the pre-curation gear
- Step 3: Edit the three spreadsheets produced by the pre-curation gear
- Step 4: Upload the edited spreadsheets to the project or subject
- Step 5: Re-run the pre-curation gear with the spreadsheet inputs specified
- Step 6: Check the acquisition labels
Step 1: Review the README for the pre-curation gear
As with many gears, the pre-curation gear is in active development and may have new features that you have not seen or used before. Additionally, since it can be a little confusing as to why the gear is run twice, the README provides information about the process. Review the README in Github.
Step 2: Run the pre-curation gear
Pre-curation occurs for the entire project at once. The gear may be launched from the project or a single subject. Either choice generates the same output.
Here, the subject-level is selected by clicking the person icon and then highlighting the heading, not the individual session, for the participant.
Click the Analyses tab and "Run Analysis Gear".
Run BIDS Pre-Curation with the defaults and no inputs.
Step 3: Edit the three spreadsheets produced by the pre-curation gear
Download the spreadsheets.
Edit the "new_acquisition_label" column in acquisition_labels*.csv to match the ReproIn convention. Examples of the convention can be found in the BIDS Design Spreadsheet.
Step 4: Upload the edited spreadsheets to the project or subject
Uploading the edited spreadsheets to the subject-level is shown below.
Step 5: Re-run the pre-curation gear with the spreadsheet inputs specified
Step 6: Check the acquisition labels
Once the labels in the gray headings are ReproIn-compliant, you are ready for the BIDS Curation step. The default template in BIDS Curation is now ReproIn, so you will not need to select or alter the template.
