External Email - Use Caution
On 5/26/2023 5:39 PM, Andrew Dedinas Geoly wrote:
External Email - Use Caution
Hello Freesurfer experts!
I am conducting a longitudinal GMV and CT analysis of mTBI
participants who received an experimental single-dose pharmacological
treatment. We collected GE Bravo (0.9mm isotropic) T1w data pre,
immediately after (~ 4 days after intervention) and 1-month following
the intervention.
I have been working with the recon-all longitudinal pipeline stream
(7.1.1) but have noticed pretty significant errors in terms of skull
stripping and segmentation (participants are veterans with somewhat
random lesion / atrophy patterns).
I have tested your new recon-all-clinical program (7.4.0) on some of
my worst cases and it is performing remarkably well. I am doing some
more digging into the various synth segmentation packages available in
FS newest versions and was wondering what the best course of action
would be for integrating recon-all-clinical or synthseg into a
longitudinal workflow.
1.Could I use the recon-all-clinical outputs as the "cross" for later
base and long template construction?
I don't know. Hopefully Eugenio/Karthik will weigh in
2. SynthSeg and SCLimbic seem to have very good test-retest
reliability-- would it be feasible to use the independent segmentation
extractions from those and bypass the longitudinal stream entirely
(not saying I would want to but I am curious)?
sclimbic generates segs that are not in the long stream, so there is no
long option. My experience with synthseg is that it is inferior to the
long stream on long data
Any and all help here would be greatly appreciated, and I thank you
very much for your time.
Warmest regards,
Andrew
---
Andrew D. Geoly, MS
Research Data Analyst 1
Brain Stimulation Lab
Department of Psychiatry and Behavioral Sciences
Stanford University School of Medicine
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