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thanks Douglas. That is really helpful I will try that

best fraser

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I have not tried that, but I wanted to point out that you can also use samseg, eg, samseg --i yourvolume.nii.gz --o samseg samseg/seg.mgz will be a segmentation that includes skull You can also use simnibs https://secure-web.cisco.com/13PrcHfMbn2eZQ5WJxk9WhDOqtZujgVq73h8oGn6AjH6wUJ...https://secure-web.cisco.com/1XtOWBsK8_dPhnQpfJ-kNYgmH-U-WNllAfbj959E9w0FC-B6AIpZ5jxoQf3OikVYb1MHhnpw-Kh7DAcienmVUAr7QBGY2p9yCUy9yK64fIChpB94C6S2-VynrnTVc1jGAoZiLmAG11ww9WX5BLHRZclGomZ3WGvI5R3DKigEhU_oHqgcG88aYP9sduw6xSeE7yoBQ696696VHC3VLkUlVv0jkG1UpEu2kuHv29NxHvQfyELEhvX6d-hqED937md44jJAhPqveRGXrAt_Dc5O28mtek_HChxVvg64eckGrL1I-s0Nna0b27i2rc0LQ7fpD3VhFSVAEo7wOX1DR6qRONA/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsimnibs.github.io%252Fsimnibs%252Fbuild%252Fhtml%252Findex.html%26data%3D05%257C01%257Cfraser.r.aitken%2540kcl.ac.uk%257Cb7292583d4ad41bf5f5d08db320d2faf%257C8370cf1416f34c16b83c724071654356%257C0%257C0%257C638158804434062382%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3Dm1sUozI8S%252FF6qla17t6eoJ9wfsylSzGPF%252BG3J0CY8a4%253D%26reserved%3D0 This uses samseg under the hood. It creates a specific skin layer and will probably work better on the skull.

On 3/31/2023 11:06 AM, Fraser Aitken wrote:

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Dear Freesurfer community

I have some low field T1 and T2 MRI images that I would like to use to create a head model for EEG source localization.

I have been using SynthSR to improve the images and Synthseg for the basic segmentation etc and wondered if anyone had used synthseg to extract skull and scalp as well as WM/GM/CSF etc and how this might be done ? (or if this was possible)

best wishes Fraser

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