Longitudinal Processing - Tutorial
This page will take you through the steps of processing your longitudinal data:
- Image Processing Steps (cross, base, long)
- Inspecting Results
- Post-processing steps
- Editing and Rerunning
Ater the tutorial (if you want to learn more) you can read details about the longitudinal stream at LongitudinalProcessing and about edits at LongitudinalEdits.
If you are taking one of the formally organized courses, everything has been set up for you on the provided laptop. The only thing you will need to do is run the following commands in every new terminal window (aka shell) you open throughout this tutorial. Copy and paste the commands below to get started:
setenv SUBJECTS_DIR $TUTORIAL_DATA/long-tutorial cd $SUBJECTS_DIR
To copy: Highlight the command in the box above, right click and select copy (or use keyboard shortcut Ctrl+c), then use the middle button of your mouse to click inside the terminal window (this will paste the command). Press enter to run the command.
These two commands set the SUBJECTS_DIR variable to the directory where the data is stored and then navigates into this directory.
If you are NOT taking one of the formally organized courses, klick here.
Longitudinal Image Processing
All data for this tutorial has already been processed for you (processing can take up to 24h). The only thing you need to learn in this section is the three processing steps (cross, base, long).
For example, assume you have a subject with two time points: OAS2_0001_MR1 and OAS2_0001_MR2.
[CROSS]: You would process these two images independently first (we call that cross as in crossectional analysis/processing). You end up with two directories with the names OAS2_0001_MR1 and OAS2_0001_MR2
[BASE]: Then you would run the second step to create the within subject template (also called base) and end up with a new directory. There is only one base directory per subject. We decide to name the base: OAS2_0001. Inside this directory are the results for the average anatomy of your subject across time. You don't use this data in any analysis, and only look at it for quality checking or editing.
[LONG]: Finally you would create the two longitudinal runs (the ones you are actually interested in). You end up with two more directories (these names get automatically assigned): OAS2_0001_MR1.long.OAS2_0001 and OAS2_0001_MR2.long.OAS2_0001. They contain the final, most reliable and accurate processing results.
You can now continue with the next section (inspecting the data).
If you want to come back later and learn about the exact commands for processing your data, click here.