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 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?
Institute for Clinical and Experimental Medicine
National Institute of Mental Health
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