recon-all does not do so well with data at 0.5mm. I created a high-res patch for version 6.0 as part of my support fo r the HCP. You can get it here https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp this shold work much better.
On 8/27/19 10:15 AM, Giovana dos Santos Cover wrote:
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Dear Freesurfer experts,
I am trying to segment the white and pial matter from my MR images but for some reason, the final segmentation always misses some brain areas. I attached here a nu and brainmask image with the segmentation as an example. The MR image I am using isaMEMPRAGE 0.5mm resolution acquisition from a 3T Siemens TrioTim scanner, possibly with a 64 coil channel. Can you please help me figure out how I could improve the segmentation?
I am using the following command:
recon-all -autorecon1 -autorecon2 -autorecon3 -s hires_test -hires -i high_res.nii
On another note, the full recon-all command takes around four days to finish in an 8GB ram mem computer. I would appreciate if you happen to have any suggestions on how I could run it faster, if this is even possible.
Thanks Gio.
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