Hi Lara,
no, you should not use time point 1 as base.
You need to distinguish between the image processing part and the statistics post processing analysis (LME). These are two separate things.
For the image processing in the longitudinal pipeline, we create the base (=subject template). The name base can be misleading and has nothing to do with "baseline". That is why we try to refer to it as "subject_template" in most documentation now. Anyway, one never analyzes results of the subject template, but of the final fine-tuned time points after the -long runs.
In your case, you can simply process the images independently (cross sectionally) and still perform the statistical LME analysis where you group results from the same subject.
For measures from the stats files (aseg, aparc...) you just obtain those from the cross dirs with asegstats2table. For surface results you simply map everything to fsaverage (mris_preproc) and then run the LME.
Best, Martin
On Thu, 2020-02-20 at 21:53 +0000, Lara Foland-Ross wrote:
External Email - Use CautionHi there,
Reposting this message (below). Would appreciate any guidance you can provide.
Thanks, Lara
From: freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Lara Foland-Ross lfoland@stanford.edu Sent: Friday, February 7, 2020 12:46 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] some basic questions regarding longitudinal analyses in Freesurfer
External Email - Use CautionHello,
I'm analyzing a large dataset using an LME model to examine longitudinal changes in brain structure that vary as a function of group (patients vs controls). Because some participants were scanned several years apart in early childhood, the intra-subject registration failed in the longitudinal processing stream. For this reason, my data were not initially processed using the longitudinal processing stream within Freesurfer. However, per this thread - https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg55847.html
- I still plan to use the LME model. As I understand it, this model
assumes that the longitudinal processing stream was conducted. Therefore, I have the following questions:
- would the "base" (aka within-subject template) for each subject be
= time point 1? 2. would the "long run" for each subject be = each subject's individual time points? 3. assuming #1 and 2 are correct, would I need to set my directory structure to match that used in the longitudinal processing stream? For example, if I have 2 time points for subject 1234, and they are initially labeled "1234.time1" and "1234.time2", then in order to run the LME model, I would create a copy of "1234.time1" and rename the copy as "1234" to indicate to the software that this should be used as the base. And, I would also need to rename "1234.time1" and "1234.time2" as "1234.time1.long.1234" and "1234.time2.long.1234" to indicate that these folders should be used as the longitudinal time points.
Does this seem appropriate?
Thanks in advance for your help, Lara
Lara Foland-Ross, Ph.D. Senior Research Associate and Imaging Lab Manager Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795
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