Hi Chris,
Since there is only one timepoint, the base recon-all command will look like this: recon-all -base <templateid> -tp <tp1id> -all
<tp1id> is the subjectID for the one timepoint you have. Not sure how you named <templateid>. It should be an unique name in your SUBJECTS_DIR.
Hope this helps.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Hemond, Christopher Sent: Wednesday, March 29, 2023 2:02 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Longitudinal processing of single time point data
External Email - Use Caution Dear Freesurfer experts, I am processing longitudinal data from subjects participating in a pre-post analysis; a few subjects do not have follow-up data. I'd like to still include these subjects and plan on using mixed effects analysis methods given the unbalanced data. I am following the wiki tutorials in this regard (specifically MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessinghttps://secure-web.cisco.com/1YHlXw74PCpQ3T6qawqkxxMCM_VcHyTlbf-HZnuBTtb68uuIXxLXB_5t7zOtAtZnDWU2iAiVhOM-Qg0sWs_-iJEwQQoVWur6NJapgVdeQzQQYUlhk6O3h88ue-fC6_pDJ3gmlRd_v_dqsjQBWFRvzInbw16_kEsTuzvTNEaNYY_ORuffGXYyh4Pwo1SPOPiSQ-JYykIcQWn2q2BTgBMVOJAz7u2rykJiG2aoHFLwikwgBrHomMrmV1bWH4czxaSXDOQTEQvpMDSZi7ayG6leyH_G-m2F69lFSKD3khpnLRshifw5FCcAXI-IhaSJrKfRFI2KbsbaRTQ4qL69oh7q4Zw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLongitudinalProcessing), which suggests that subjects having a single time point should be processed in the longitudinal pipeline to reduce bias (from Bernal-Rusiel 2013). From the webpage: "Single time-point subjects: Because of drop-outs it can happen that some individuals were scanned only at a single time point. Instead of removing this valuable information, it is possible (e.g. in the linear mixed effects models LME) to include this data. For that it, however, becomes necessary to run the single time points through the longitudinal stream, to ensure that also those images undergo the same processing steps. This can be done by simply passing a single time point in the base creation step"
On a single-timepoint subject I ran: "recon-all -base <subject_base> -tp <baseline_timepoint> -all
However I get the following error: ERROR: It appears that the -base templateID that you passed: -base <subject_base> is an existing regular (cross sectional) run! Please make sure you pass a new name (not one of the time points) for the template with -base.
I've searched the archive but didn't find anything with this. Maybe I am doing something obviously wrong! Any help you could provide would be greatly appreciated. I'm running freesurfer-darwin-macOS-7.3.2-20220804-6354275.
Many thanks, Chris
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