The first thing to do is to re-run you data using different subject names so that you have an unedited version. You can then use mri_diff, eg, mri_diff unedited/mri/wm.mgz edited/mri/wm.mgz to determine if there is a differenece that you are just not seeing
On 9/27/2021 7:16 PM, Kevin Miller wrote: > External Email - Use Caution > > Hi, > > I am new to recon-all and Freesurfer and I am having some difficulty tracking > down the resulting outputs from when I re-run recon-all or they are not > taking hold. So far I have edited two subjects after the initial run by > lowering the ws height for the skullstrip in one and by adding white matter > voxels by in the other. I followed all the tutorial instructions for both, > starting with the edits and including the appropriate recon-all commands, > which supposedly finished without error. However, after viewing the new > volumes that were overwritten the day they were run, neither seem to have > changed. For the wm.mgz, even, the wm voxel edits still exist as though > recon-all did not run. If anyone has any tips for finding the proper outputs > or what I might be doing incorrectly, I would greatly appreciate any advice. > > Thanks > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
