Re: [Freesurfer] Running FreeSurfer with fmriprep

It looks like the data are fairly low quality. This will require some manual intervention (control points, fixing topologogical errors, etc). See our wiki on manual interventions

On 6/15/2021 10:52 AM, Rosalia Dacosta Aguayo wrote:

External Email - Use Caution

Here is what I am referring to:

On Mon, Jun 14, 2021 at 7:47 PM Rosalia Dacosta Aguayo <rdacostaa@gmail.com mailto:rdacostaa@gmail.com> wrote:

Dear Freesurfer's experts,


I have run recon-all all to one subject with fmriprep.

The work finished without errors. However, after inspecting the
results, I have seen that there are some *grey regions* (mainly
frontal and temporal ones) that have not been fully covered.

I wonder how I could proceed in order to improve the segmentation.

Kind regards,
Rosie

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