Hippcampus actually looks like it might be ok; are those holes actually
ventricle? I don't see a caudate label on there. Thalamus can often be
underlabeled as there is so much WM in it. You can try running the
thalamic nuclei segmentation, eg,
segment_subregions thalamus --cross subject
This will segment the nuclei, but you can just merge them all together
to get the whole thalamus seg
On 1/30/2025 3:18 PM, Jeong Yeon Kang wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I am attempting to run recon-all on a group of nifti T1’s (parameters
listed below). All the T1’s look good (no noticeable artifacts) and
the cortical parcellations work well, and log files say completed
without error. However, when looking at the subcortical segmentations,
the thalamus, caudate and hippocampus appear consistently under
segmented (screenshots below).
T1 MRI: 1.5 Tesla GE Signa HDxt scanner with an 8-channel head coil,
using a three-dimensional fast spoiled gradient echo (3D-FSPGR)
imaging sequence, with 188 sagittal slices scanned using the following
parameters: repetition time (TR) = 11.70 ms, echo time (TE) = 5.12 ms,
inversion time = 500 ms, flip angle = 8°, matrix size = 256×256, slice
thickness = 1 mm, in-plane resolution = 1 mm^2.
We have tried a number of preprocessing steps on the T1 images but
none of them appear to significantly improve the subcortical
segmentations:
1. Normalizing the intensity of T1 voxels
2. Running FreeSurfer versions 5.3, 6, and 7
3. FastSurfer
4. DeNoising using ANTS
5. Bias field correction using ANTS
We did not find anyone with similar issues in the archive so any
insights or guidance would be much appreciated.
Sincerely,
Melody
--
*Melody Jeong Yeon Kang*
Ph.D. Student
Imaging Genetics Center
*USC* Stevens Neuroimaging and Informatics Institute
Keck School of Medicine of *USC*
University of Southern California
Email: jkang...@usc.edu
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