The next version of FreeSurfer should have several of these improvements implemented in it. We don't have a longitudinal processing stream set up for the HCP Pipelines at this time. What might make the most sense is to run each visit separately through the pipelines and then run the longitudinal FreeSurfer stream (which I believe requires prior runs of recon-all on each visit.
Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of Antonin Skoch <[email protected]<mailto:[email protected]>> Date: Tuesday, October 18, 2016 at 3:14 PM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] HCP pipelines with FreeSurfer longitudinal stream? Dear experts, I am considering the best option how to process the structural MRI data of our longitudinal study. We have patients and controls, each subject was scanned twice. Our data meet the requirements of HCP pipelines which I would prefer to use. On the other hand, in FreeSurfer there is a special designed "longitudinal stream" for this purposes: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing Since the FreeSurferPipeline.sh, FreeSurferHiResWhite.sh and FreeSurferHiResPial.sh mostly invoke FreeSurfer routines, there should be an option to modify these scripts to do the "longitudinal reconstruction". In most of recon-all invocations there should suffice to add directives for longitudinal stream, but the modification of FreeSurferHiResPial.sh and FreeSurferHiResWhite.sh is more tricky. I am not sure how to properly set all the parameters of mris_make_surfaces there. Do you have someone the modified scripts available or can provide guidance for proper modification of standard scripts? Regards, Antonin Skoch Institute for Clinical and Experimental Medicine National Institute of Mental Health Czech Republic _______________________________________________ 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
