This describes how to process rCBF data produced by the Siemens scanner using their pulsed ASL (PASL) protocol in the FreeSurfer environment, including registration and group analysis. This is sequence is usually called "ep2d_pasl". If you are not using this sequence, this information is NOT for you. This sequence will produce a several series, one of which will have "relCBF" as the series description. It will have one time point.
There are two programs that will be used here: rcbf-prep and rcbf-merge, each has its own help which you can see by running with --help.
The output relCBF will be in mL/100g/min.
The analysis will be done in two or three stages. First, analyzing each individual subject with rcbf-prep. Second, merging all the individual results with rcbf-merge. Finally, if you want to perform group analysis, then you will use mri_glmfit.
Individual Analysis (rcbf-prep)
For each subject, run the following command: