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Can you give some details on the DTI sequence you are using for this study? Generally, monkey EPI DTI scans will require some distortion correction before they can be accurately registered to a T1 image. Peace, Matt. _____ From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of MCLAREN, Donald Sent: Wednesday, March 05, 2008 6:07 PM To: [log in to unmask] Subject: Re: [FSL] Registering Monkey I actually haven't tried registering T1-weighted scans and DTI scans as of yet; just T2-weighted and T1-weighted scans. (1) Have you tried using both the FA and I0 images to do the registration, I'm wondering if changing the DTI image would improve the results. (2) What are your voxel resolutions of the DTI and T1-weighted images? (3) Do you have a T2-weighted image? (4) Are you using a 6-parameter affine transformation? (5) Can you attach a image of the poor registration? On Wed, Mar 5, 2008 at 4:01 PM, Roman Loonis <[log in to unmask]> wrote: It does not seem to be cutting brain tissue from outside the brain. I am trying to register a monkey anatomical scan to a monkey diffusion scan. Roman On Wed, Mar 5, 2008 at 1:34 PM, MCLAREN, Donald <[log in to unmask]> wrote: (1) Check the BET output to make sure that it is not cutting off any brain tissue or including anything outside of the brain. (2) What are you trying to register? On Wed, Mar 5, 2008 at 12:29 PM, Roman Loonis <[log in to unmask]> wrote: I am trying to do tractography on monkey brains using FSL studio. I obtained my images in minc, did some preprocessing, and registered them in minc. I checked visually to make sure the the structural was well registered with the diffusion images in a minc based software. I subsequently converted the files into proper nifti files. Following this converison, my files were no longer registered properly... I am not too sure what kind of fix there is available for this error. Moreover, I tried registering the images using FSL's Bet extraction and then the "registeration" program. The files after the registration were not well registered. What should I do? -- Best Regards, Donald McLaren ===================== D.G. McLaren University of Wisconsin - Madison Neuroscience Training Program Tel: (773) 406 2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406 2464 or email. -- Best Regards, Donald McLaren ===================== D.G. McLaren University of Wisconsin - Madison Neuroscience Training Program Tel: (773) 406 2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406 2464 or email.