Re: [HCP-Users] Minimal Preprocessing Pipelines

[Glasser, Matthew]

Probably need to specify your probtrackx2 command lines, but both rigid alignment to MNI space and nonlinear alignment are available in the ${StudyFolder}/${Subject}/T1w and ${StudyFolder}/${Subject}/MNINonLinear locations respectively.   Peace, Matt. From: <Archer>, Derek B <arche...@ad.ufl.edu> Date: Monday, May 18, 2015 at 12:54 PM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] Minimal Preprocessing Pipelines Hello,   For the diffusion data, are both FLIRT and FNIRT completed in the minimal preprocessing script?  I am doing tractography on relatively small tracts, and there seems to be high variability in the placement of the substantia nigra, putamen, and other regions.    Thanks, Derek Archer _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org 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 HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users