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.



 on behalf of Antonin Skoch <<>>
Date: Tuesday, October 18, 2016 at 3:14 PM
To: "<>" 
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 

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:

Since the, and 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 and 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?


Antonin Skoch
Institute for Clinical and Experimental Medicine
National Institute of Mental Health
Czech Republic

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