The output FA image shows too many high value spots

[aghayoor]

Hi team,

I ran the qsiprep with --recon_spec dsi_studio_gqi. Here is the full command line:

qsiprep-docker $datadir/BIDS/ $outdir participant --recon_spec dsi_studio_gqi --participant-label 01 --output-resolution 2 --fs-license-file ./fs_license.txt --verbose --verbose -- stop-on-first-crash

All DTI metrics are generated in /qsirecon/dwi/ directory. However, the output FA image shows several high value spots scattered all over the image. A screenshot of all views is attached here.

I appreciate your help and comments here.

Thanks, Ali

[aghayoor]

Hi @mattcieslak ,

Do you have any idea about the issue reported here? Also, I am interested to get the colorFA, which of the default recon_specs do you recommend to use? I have attached the .json file of the raw dwi here.

Thanks, Ali

sub-01_run-01_dwi.json.txt

[mattcieslak]

The high values of FA are from poor model fits, I believe. I don't have a recon spec that creates a colorFA file. If you're looking to do DTI-centric analysis, you can use the --recon-spec reorient_fslstd and run them through the FSL tools.