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Hi FSL experts, I ran the whole tbss pipeline. All finished without (apparent) error. However, my all_FA_skeletonise hat holes in it. Doing a more thorough QC, I found: QC after tbss_1_preproc -> was fine QC after tbss_2_reg -> some of the brains were distorted I checked the dti_FA.nii.gz images of the affected subjects but they look okay; same is true for these images after running through tbss_1_preproc. I'm running tbss_2_reg again... but this might result in the same. Any idea what else I could try or why this error is happening? I would be grateful for some ideas! Cheers, Steph ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1