| Hi Freesurfer People, I’m working on a 2015 Macbook Pro with OS X El Capitan version 10.11.2 and I have System Integrity Protection disabled (though I hadn’t experienced any issues that could have been a result of that function). Everything in FreeSurfer works fine for me—I ran recon-all and successfully processed dicom files, I successfully viewed the T1.mgz and brainmask.mgz volumes and the pial and white surfaces, and I successfully deleted unnecessary voxels and added a set of control points (in both cases, being careful to make and save the changes on all necessary slices with the brainmask volume highlighted). My only issue is that when I reprocess the data using recon-all -autorecon2-cp -autorecon3 -subjid <my subject ID>, it runs through the reconstruction without error and then shows no changes at all in freeview when I view the volumes/surfaces. The deleted voxels still appear deleted and I can still load the control points, so why wouldn’t it make the changes? And just to provide a little extra info: I encounter the same problem when I reprocess the tutorial data for the pial edits tutorial. I delete the voxels as instructed, save the file, reprocess it without error, and then nothing’s changed when I view it all again in freeview. Any help would be HUGELY appreciated—I’ve stressed over this for weeks trying to get my computer to function properly so that I can begin my work as a research assistant in a neuropsych lab editing and analyzing brain scans with FreeSurfer. Thanks, Champe |
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