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,

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:

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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: jkang395@usc.edu

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