Have a look at the example script: https://github.com/Washington-University/HCPpipelines/blob/master/Examples/Scripts/PostFreeSurferPipelineBatch.sh
I have just fixed it to default to MSMSulc in the latest master. As for 0.9mm T1w and T2w data, you could make 0.9mm templates of the various files if you wanted (or use the 0.8mm version). flirt -applyisoxfm 0.9 would do it. Be sure to use spline interpolation for images and nearest neighbor interpolation for masks. Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Shachar Gal <gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>> Date: Sunday, August 26, 2018 at 2:34 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Cc: Niv Tik <niv...@gmail.com<mailto:niv...@gmail.com>> Subject: [HCP-Users] PostFreeSurfer Pipeline Hello, Before running the PostFreeSurfer pipeline on our data, we had some questions - 1) If our T1 resolution is 0.9 mm, and not 0.7 (like the HCP data), will we encounter a problem during the process of registration back to the native space using this pipeline? 2) We would appreciate a clarification regarding the variables that are needed for this script to run (added bellow). we figure that most of the paths are found in the 'global' dir, but not sure exactly which. SurfaceAtlasDIR GrayordinatesSpaceDIR GrayordinatesResolutions HighResMesh LowResMeshes SubcorticalGrayLabel FreeSurferLabels ReferenceMyelinMaps CorrectionSigma RegName InflateExtraScale Thanks, Shachar Gal, Tel Aviv University _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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
