[RESOLVED] Bias correction pre_freesurfer step

Use Questions
1

Hi everyone,
I want to do a bias correction on the pre_freesurfer step. I’ve seen a parameter in the hcp_pre_freesurfer T1wBiasCorrect that is set as empty. Is there a way to set it true? I cannot find anything inside qunex wiki.

Best regards,
Chiara

2

Chiara, hi!

Looking at the HCPpipelines code, specifically the PreFreeSurferPipeline.sh, which QuNex calls, the script indeed does report T1wBiasCorrect parameter in the log, however, the parameter is not set or used anywhere in the script. For that reason, you can not set it through QuNex either. Bias field correction of T1w image (and T2w image, if available) is performed by default and can not be turned off by a parameter.

With kind regards,

Grega

1 Like
3

Hi Grega!

thank you so much for your answer!

kind regards,

Chiara