Hi, I don’t think the following is necessarily your problem, but know that the simple tensor model is not appropriate at high b-values. You should either 1) use the “—kurt” or “—kurtdir" flags which will add a “mean kurtosis” or “parallel/perpendicular kurtosis” parameters that can account for non-exponential decay or 2) limit the fitting to just the b=1000 shell (+ b=0’s).
cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: [email protected] From: <[email protected]> on behalf of "Glasser, Matthew" <[email protected]> Date: Tuesday, October 31, 2017 at 3:57 PM To: "Archer,Derek B" <[email protected]> Cc: "[email protected]" <[email protected]> Subject: Re: [HCP-Users] Inaccurate b0 Image from DTIFIT That cannot be the command line as not all the parameters are present. I agree that picture looks incorrect. Does this happen consistently across subjects? What subject is this? Peace, Matt. From: "Archer,Derek B" <[email protected]<mailto:[email protected]>> Date: Tuesday, October 31, 2017 at 3:06 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Subject: RE: [HCP-Users] Inaccurate b0 Image from DTIFIT Hi Matt – I am only using one line of code, which is: dtifit –mask=nodif_brain_mask.nii.gz –bvecs=bvecs –bvals=bvals –gradnonlin=grad_dev.nii.gz –out=prefix. This is the exact line of code I run with data from our group, but instead of giving bright ventricles it’s dark. I’ve attached an image of the Human Connectome data. Derek B. Archer Postdoctoral Research Fellow Laboratory for Rehabilitation Neuroscience (812) 259-0687 From: Glasser, Matthew [mailto:[email protected]] Sent: Tuesday, October 31, 2017 3:08 PM To: Archer,Derek B <[email protected]<mailto:[email protected]>>; [email protected]<mailto:[email protected]> Subject: Re: [HCP-Users] Inaccurate b0 Image from DTIFIT Please post the two command lines and some example images. Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of "Archer,Derek B" <[email protected]<mailto:[email protected]>> Date: Tuesday, October 31, 2017 at 11:56 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] Inaccurate b0 Image from DTIFIT Hello all – I am working on running DTIFIT on human connectome project diffusion data, but when I run the code using the gradnonlin option, the b0 image doesn’t look correct. On a typical b0 image, the ventricles should be bright. The output on all of my subjects gives me dark ventricles. Is this inaccurate? Does DTIFIT work corrected with high b-values? Thanks! Derek B. Archer Postdoctoral Research Fellow Laboratory for Rehabilitation Neuroscience (812) 259-0687 _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users<https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers&d=DwMF-g&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=WzWugqmdiAiNoLF3h2MO4NlpXjl1PyEMfbssfNlbDZM&m=LnppAu7qltKOPCx9KNcSIsywbLXMn-KzeNO7EidFzvo&s=bT2z2SzWDrqmA0HHCOTiJTQq-cHE6MwibvSrrrXgWY4&e=> _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
