Dear Nima,
Thanks for the interest in our work.
I don’t know if I would advise trying to segment these small subregions from
such thick slices. But if you are set on doing that, I would probably run
SynthSR first, and work with the synthetic 1mm isotropic T1s. You can run
SynthSR on the T1s and
Dear FreeSurfer Community,
I’m currently working with clinical MRI data and would appreciate your guidance
regarding two issues I'm encountering with hippocampal/amygdala segmentation
(segmentHA_T1.sh script). My available T1w and T2w scans both have 6 mm slice
thickness and are anisotropic and
Hi Ivan,
Thank you for your interest in SynthStrip. A Dockerfile is only executed once,
when you build ("compile") the container, not when you run it. You may want to
consider writing a simple Python or shell script that loops over your files and
calls the existing container on each.
Do you ha
Hi Stefanie
The registration is based on the curvature of the smoothwm surface (among other
things) so not easily. Lilla might know more about that atlas.
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Stefanie Bradley
Sent: Monday, March 31, 2025 4:35 PM
To: freesurfer@nmr.m
External Email - Use Caution
Hi FreeSurfer experts,
I am using the univariate LME pipeline (lme_fit_FS & lme_F) to conduct cortical
thickness analysis on a subset of D-K atlas ROIs between two groups. Although I
am testing longitudinal group*time differences with this pipeline,
