External Email - Use Caution
Here is the tutorial page for longitudinal pipeline -
https://secure-web.cisco.com/1DcUJ0a_skONZSHVRpSGkgbTHuJUYN0f05kxjKkGh8ULxXW5lqtpzszfBoN-Xtfji8oIhv9vRccou8zbWsrBEOjLdmo0rTMcvCMZxYlfgwwj9WhTkMxZjPQXRIllql_rFkKSHG62EwrEuQ-E69bA0inHgOQJ7ZBwMv0T0u6l4NK6aCGAw_C5Dz8H3TS_qFlJDhaFv6Z1RzMJDTcBIPCGKbIPF8cz0m_l0mkH528Meg0J0mttU67tqAWOdr3KFVBAtTpqx8axSHsTpQG_Bs18idA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLongitudinalProcessing
In step 1 (cross), recon-all -all -s <tpNid> -i path_to_tpN_dcm
you should have processed each of your time points separately, for example,
<tpNid> = tp1, tp2, tp3 (these are the subjectIDs you choose for your
subject/timepoint).
In step 2 (base), recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all
1. Choose an unique subjectID as your <templateid> (for example,
base_tp1_tp2_tp3).
2. -tp <tp1id> ... are the subjectIDs (tp1, tp2, tp3) from your cross process.
In step 3 (long), 'recon-all -long <tpNid> <templateid> -all'.
It should output in directory <tpNid>.long.<templateid>.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Atwater, Emanuel R
Sent: Thursday, July 27, 2023 6:15 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] (no subject)
External Email - Use Caution
Hello FreeSurfer Team,
I recently messaged about running a longitudinal scan on a couple of images.
The response told me to utilize "timepoints":
For base processing, specify each timepoint with -tp <> (not the nii file).
recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all
I've attempted to review the youtube videos and instructions made available
online but am unsure what "timepoints" are. Can I have some clarification on
what exactly a timepoint is, please.
FS version: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b
Recon-all.log: see attached
V/r,
Emanuel Atwater
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