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Hi FreeSurfer Developer,

I am using FreeSurfer to analyse cortical thickness and ROIs volume. My input MRIs brain format is – nii.gz ( converted from T1 .dicom).

I managed to run recon-all without any errors in some of my subjects. But, I am encountering the following error when I run recon-all on the other half of my subjects ( all are the same error) : Recon-all -s subject05_post exited with ERRORS. Error : found no voxels matching id 1 Found : 0 label voxels

I have tried both watershed and no skull strip to tackle it. But it still finished with the same error. I have also tried running recon-all in separate stages – autorecon 1 , autorecon 2, autorecon 3 – the error seems to happen in autorecon 2 stage.

I have searched the list, and no similar error was reported.

Could you help me troubleshoot this error? ( I am also quite new to the field of MRI analysis and using FreeSurfer)

I’m using FreeSurfer version 8.0.0 Platform – Mac OS Sequoia version 15.5 , Memory 36 GB, Storage – 370 GB Recon-all log : please see the attached. I have also attached the input nii.gz file to this email.

Thank you.

Yours sincerely,

Dr Win Khine Clinical Research Fellow Imperial College London