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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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/LongitudinalProcessing<https://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
The information transmitted is intended only for the person or entity to which
it is addressed and may contain confidential and/or privileged material. Any
review, transmission, re-transmission, dissemination or other use of, or taking
of any action in reliance upon this information by persons or entities other
than the intended recipient is prohibited. If you received this in error,
please contact the sender and delete the material from any computer.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
