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 <tpNid> -i path_to_tpN_dcm

2. recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all

3. recon-all -long <tpNid> <templateid> -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 ___________________________________ Karolinska Institutet – a medical university

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