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" <arche...@ad.ufl.edu<mailto:arche...@ad.ufl.edu>> Date: Tuesday, October 31, 2017 at 3:06 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> 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:glass...@wustl.edu] Sent: Tuesday, October 31, 2017 3:08 PM To: Archer,Derek B <arche...@ad.ufl.edu<mailto:arche...@ad.ufl.edu>>; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Inaccurate b0 Image from DTIFIT Please post the two command lines and some example images. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Archer,Derek B" <arche...@ad.ufl.edu<mailto:arche...@ad.ufl.edu>> Date: Tuesday, October 31, 2017 at 11:56 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> 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 HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> 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 HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
