[RESOLVED] Low fractional anisotropy value

Dear Jure and Lining:

I ran into a problem (exceptionally low fractional anisotropy maps. e.g the corpus callosum only has FA of about < 0.3) with my data that was acquired with the HCP aging protocol. I have attached the scripts that I used for running the preprocessing (script_to_run_steven_chau.txt) and diffusion postprocessing (script_to_run_diffusion_steven_chau.txt). And you can download the data (link) to reproduce the problem.

I couldn’t really figure out where the problem was, and your help would be greatly appreciated as always!


006_batch.txt (5.0 KB)
006_mapping_steven_chau.txt (328 Bytes)
script_to_run_steven_chau.txt (4.8 KB)
script_to_run_diffusion_steven_chau.txt (3.1 KB)

Hi Ed,

It sounds like you successfully ran hcp_pre_freesurfer, hcp_diffusion, and dwi_DTIFIT without error. The QuNex commands for hcp_diffusion and hcp_DWIFIT look okay to me. The link you posted with the example data has expired so they’re no longer available to view. Have you run the QuNex QC commands ( i.e., qunex run_qc with modality=‘DWI’)? How does your processed diffusion and FA data look (e.g., dti_FA.nii.gz)? Does your WM masks align well on the brain (e.g., does your CC mask overlap on the ventricles)?