Dear FreeSurfer experts,
We have a longitudinal study design with up to 5 time points. However, we both want to do a baseline cross-sectional analysis and later a longitudinal analysis. All subjects have been run through the longitudinal pipeline (only the base was edited). We want to start analysing baseline cross-sectionally using QDEC. I have read through the wiki guides but would like to make sure that we are doing it correctly. We have done/plan to do the following:
1. The [CROSS], edited [BASE] and [LONG] is processed.
2. We will create a qdec table called qdec.table.dat. However, because we want to use the improved longitudinal runs [LONG] (i.e., because the [BASE] has been edited] the first column in the QDEC table (i.e., fsid) has been changed to include the longitudinal names (please see below). In addition, we have included the line *SUBJECTS_DIR /my/path/to/subject/data* to let FreeSurfer know that it is the longitudinal directories that should be used (is this the correct why to let FreeSurfer know that it is the "longitudinal runs" which should be used?).
SUBJECTS_DIR /my/path/to/subject/data fsid Gender Group Age d115a.long.d115_base 1 1 19 d120a.long.d120_base 0 1 22 ...
2. We transfer the default fsaverage to the subject directory. 3. To presmooth the data onto the target we run the following command: *recon-all -long <tpid> <baseid> -qcache*
When the above steps are done we plan to load it into QDEC.
Is the above steps correct for doing a cross-sectional group analysis in QDEC?
Best regards, Kasper Jessen MD, PhD student