Re: [HCP-Users] Q about use of normalization params

[Harms, Michael]

Hi Matt, If John is trying to project a native space parcellation onto the fMRI, don’t you want the -r argument to be something like the MNINonLinear version of the SBRef instead of the MNINonLinear version of the T1w scan? --  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: mha...@wustl.edu From: <hcp-users-boun...@humanconnectome.org> on behalf of "Glasser, Matthew" <glass...@wustl.edu> Date: Thursday, January 21, 2016 at 2:35 PM To: John Griffiths <j.davidgriffi...@gmail.com>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Q about use of normalization params applywarp --interp=nn -i <your input> -r ${StudyFolder}/${Subject}/MNINonLInear/T1w_restore.nii.gz -o <your output> -w ${StudyFolder}/${Subject}/MNINonLInear/xfms/acpc_dc2standard.nii.gz Peace, Matt. From: <hcp-users-boun...@humanconnectome.org> on behalf of John Griffiths <j.davidgriffi...@gmail.com> Date: Thursday, January 21, 2016 at 11:48 AM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] Q about use of normalization params Dear HCP Peeps,  I have a parcellation in native space that I would like to project to MNI space. It seems from the Pipelines code that this is taken care of by OneStepResampling.sh, but I can't quite distill the legion inputs and outputs of this command down to the flirt inputs and flags I need. So, specifically, what would be the flirt command to project  T1w/T1w_acpc_dc.nii.gz to MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_hp2000_clean.nii.gz (presumably this is just the projection to MNINonLinear/T1w.nii.gz + reslicing to fMRI target?) Things I'm not sure of: - location of the correct affine registration .mat file - which nonlinear warps - reslicing to fMRI dimensions (target image, or just tell it the dimensions?) - other stuff I might have missed Thanks,  John -- Dr. John Griffiths Post-Doctoral Research Fellow Rotman Research Institute, Baycrest Toronto, Canada and Honorary Associate School of Physics University of Sydney _______________________________________________ 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   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