Hi, I may have a suggestion for this problem. The problem is that the registered b0 image was not matched to the T1? In the flirt, you could try -searchrx -searchry -searchrz and change the default setting from "-90 90" to "-180 180". I hope it could work. Best | | Szhang | | | On 11/14/2018 22:08,Josh Robinson<[log in to unmask]> wrote: Hello FSL experts, I am using FDT to process DTI data to do probabilistic tractography. Currently I am FLIRTing the b0 to the subject t1, and then FLIRTing and FNIRTing the subject t1 to a template t1. When using FLIRT and FNIRT for the t1s, I find that my in and ref images have different orientations on the LR axis, as read by fslhd. Heeding the many warnings against using fslswapdim, I was wondering if it would instead be possible to use fslreorient2std on the data? I am hesitant as I would think I would need to reorient the diffusion data as well and this would also require reorienting the bvecs? Is this accurate? Is it even necessary for this orientation to match? I have read in other threads that FLIRT can *usually* find the right registration even if the orientations do not completely match. Any help is much appreciated. Josh ######################################################################## 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