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Dear FSL experts & Daniel, I'm encountering exactly the same problem with a data set of 300 patients with schizophrenia and healthy controls. All images before tbss_2_reg look fine, but a significant amount of subjects is extremely distorted after tbss_2_reg which then results in the FA_skeletons having holes in them. What could we try to improve this step? Thanks in advance for your help! Stephanie -----Ursprüngliche Nachricht----- Von: FSL - FMRIB's Software Library [mailto:[log in to unmask]] Im Auftrag von Daniel Callow Gesendet: Donnerstag, 6. Dezember 2018 21:40 An: [log in to unmask] Betreff: [FSL] tbss_2_reg poor registration Hello FSL experts, I am working with a dataset of 30 older adults scanned twice on a 3T SIEMENS scanner and am trying to run tbss analysis on the data. Eddy correction and dtifit seem to have worked pretty well for the most part, however, my tbss outputs come out pretty poorly. I have run two separate tbss analysis on the data. One of which I use FA58 as the target and the other in which I use the selected most "average" FA image. The issue I seem to be having is at the point where I run tbss analyses using tbss_2_reg -n and -T flags. For both analyses, the registration and warping are pretty poor. Especially when using the FA58 target, some of the image registrations are alright but a good number of the outputs seem to be completely ruined. As for the self-selected target analyses, the registration and warping seem to be a bit better. than for FA58 However, they still seem to be pretty bad and the all_FA, all_skeleton, mean_FA, and mean_skeleton outputs aren't nearly as nice as I would expect them to come out. Does anyone have any tips for improving this step? Have any of you heard reasons the linear and nonlinear registrations might work so poorly and thus, have potential troubleshooting ideas? Might some further preprocessing alignment steps help the registration process? Thank you for any advice and input you can provide! Daniel Callow ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1