Hi Akram, I have access to that directory, but those logs don't seem to be there. What was the exact command you ran using dtrecon? Thanks, Dennis

Akram Bakkour wrote:

Hello, freesiffusion-support@nmr.mgh.harvard.edu doesn't seem to exist, so I'm hoping one of you can help me out. I seem to be having trouble with the -mask 0 flag in dtrecon. It doesn't apply a brainmask! I tried -mask 1 but that didn't work either. I unpacked the data properly, then ran diff-flirt -i f -o unwarp/f -tmpdir tmp for motion and eddy current correction and then ran dtrecon -i f -o maps -mask 0 but my maps/fa volume is not brain masked. Here are the logs: /space/thigpen/10/users/min/OFRR27/dti/025/unwarp/dtrecon-22259.log /space/thigpen/10/users/min/OFRR27/dti/025/unwarp/raw2tensor-22289.log /space/thigpen/10/users/min/OFRR27/dti/025/unwarp/tensor2eig-22447.log

I can see where it says Calculating background fraction ... brain is 100% of volume nonbrain is 0% of volume

but I still don't understand why it's not working. I even tried running dtrecon on the unpacked data without running diff-flirt, but no luck.

Any and all help is highly appreciated. Thanks! Akram. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer