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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