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Ah, all the ones with v.mgz used the bigventricles option… Must be something to do with that.

Simon

From: Simon Jones spj24@cam.ac.uk Sent: 13 November 2018 21:35 To: freesurfer@nmr.mgh.harvard.edu Subject: QA_tools do not find v.mgz

I have run some Freesurfer 6 recon-all processed data through the Freesurfer QA analysis QA_tools_v1.2. The output looks mostly good but I repeatedly see these errors.

ERROR: Subject a1 missing output file ../mri/v.mgz ERROR: Subject a1 missing output file ../stats/wmsnr.e3.dat

I do actually find 100% of wmsnr.e3.dat files so that may not be a problem. But only 41% of my subjects have a file called v.mgz. This looks like ventricles prior to aseg processing. I do not find the file v.mgz referenced in any of the recon-all log files or help pages. I don’t think I have been aware of this file previously.

Why are many subjects missing this file and should I worry about it.

Thanks for your help,

Simon