Yes, I have this exact same problem. I have uploaded two rounds of data for review to the ftp service a week or so ago and I believe they are being reviewed.

After several days of testing on my end with various permutations of flags and cross and long runs and intervention points I didn’t see a single white matter surface change to reflect any edits.

I used this exact same protocol on a very large dataset (N>300) using only cross runs on Freesurfer 5.3 on Linux about 1.5 years back and didn’t have this problem. I have tested this latest dataset on both Mac and Linux, 5.3 and 6.0, cross and long, and nothing has changed the white matter surfaces.

I’m really baffled.

Best,

David P. Semanek, HCISPP Research Technician, Posner Lab Division of Child and Adolescent Psychiatry Columbia University Medical Center New York State Psychiatric Institute 1051 Riverside Drive, Pardes Bldg. Rm. 2424 New York, NY 10032 PH: (646) 774-5885

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From: Octavian Lie octavian.lie@gmail.com Date: Monday, April 3, 2017 at 11:26 AM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu, Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] wm edits not incorporated

Dear Bruce,

I just transferred subject r02.tar.gz. Again, wm.mgz edits (all deleted voxels, no additions) are not incorporated on reruns using any of the recon-all -autorecon-wm -aitorecon3 recon-all -autorecon2 -autorecon3 recon-all -make all

For example, the complete command line for a rerun on this particular subject is

recon-all -autorecon2-wm -autorecon3 -3T -bigventricles -cw256 -subjid r02 -parallel > output.txt &

Here are some of the edited voxels which are not excluded from the wm on rerun:

-40.14, -2.67, 116.29 coronal slice 132 12.73, -23.67, 126.16 coronal slice 171 14.05, 12.33, 11.61 coronal slice 147

I mention this is not the only subject where I have this problem. Thank you for your help. Octavian