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:
<[email protected]<mailto:[email protected]>>
on behalf of John Griffiths
<[email protected]<mailto:[email protected]>>
Date: Thursday, January 21, 2016 at 11:48 AM
To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
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
[email protected]<mailto:[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
