Hi Gustav,
use -all and -mprage for all steps
use -qcache and -hippo..subfields only in the -long step.
Best, Martin
On 04/25/2017 12:51 PM, Gustav Mårtensson wrote:
Hi,
I have a question regarding the longitudinal pipeline.
We are following the workflow summary as outlined in
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing,
essentially:
1. recon-all -all -s -i path_to_tpN_dcm
2. recon-all -base -tp -tp ... -all
3. recon-all -long -all
We tend to run -all -mprage -qcache -hippocampal-subfields-T1
-brainstem-structures in our cross-sectional process. Should we use
all (or part of) these options for step 2 and 3?
We are running on Ubuntu 16.04 LTS with FS version
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c.
Thank you for your help!
Gustav Mårtensson
--
*Gustav Mårtensson* | PhD student
Division of Clinical Geriatrics
Department of Neurobiology, Care Sciences and Society
Karolinska Institutet
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