On 6/25/2025 4:58 PM, Mahta Abbaspour wrote:
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Hi,
I had a question regarding how FreeSurfer handles high-resolution MRI
scans. I understand that it typically accepts isotropic 1 mm scans
(and up to 1.5 mm). I wanted to confirm whether using the -hires flag
alone is sufficient for processing this type of data, and if there are
any additional considerations I should be aware of when reviewing the
outputs.
Yes, it is. You can also use -conf2hires which uses a hybrid approach
which can sometimes be more robust (and runs faster).
I’m using v8.0.0. and working with a dataset acquired at 0.5 × 0.5 × 1
mm resolution. I used the -hires flag with recon-all, and FreeSurfer
preserved the resolution and resampled it to isotropic 0.5 mm voxels.
Also, does using high-resolution data affect the alignment or
reliability of atlas-based parcellations (like Desikan-Killiany),
given that those templates were originally developed on
standard-resolution scans?
It should have no effect because recon-all attempts to keep the mesh
resolution the same regardless of voxel resolution.
Thank you for your help.
Best
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