External Email - Use Caution The mri_diff command did show differences after re-running the wm and skullstrip commands under different names, but the differences were not related to the areas that I was troubleshooting. For example, I took the skullstrip ws height down to 10 for an adult brain in order to remove a piece of skull obscuring the temporal lobe, but it still exists in the brainmask.mgz and the mri_diff only caught one unrelated difference. Gcut missed the portion of skull as well. The same unrelated differences occurred for the wm edits and the wm.mgz still includes the wm edits from before I ran recon-all to correct it.
> On Oct 1, 2021, at 11:02 AM, Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > > 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://secure-web.cisco.com/1LdMfeu4JFsTIH46hB2dRaFccKvMDceI0wa1WvEZ9kurqMzjfM4CfBNv7zIv6fE-Mh-KrQTY18ZXj2M0IUVs8F3qBt19LEoOavUBmkRUVs3ubOdh5TcIRpA5qaPjQuElco2ddFyQk6KSu7JVMr_IYVJOw0lB-YNs1TMBKi5AMm0rfj817dIVofpD6w4HU9_2c2KZREB3e5q-quInjKSxTlsMwh1xbahLy5xCMpe6293UVwqx7oLQEAc_ldOIbaev9dFBfHz4LqecrPEC2C_OUGg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1LdMfeu4JFsTIH46hB2dRaFccKvMDceI0wa1WvEZ9kurqMzjfM4CfBNv7zIv6fE-Mh-KrQTY18ZXj2M0IUVs8F3qBt19LEoOavUBmkRUVs3ubOdh5TcIRpA5qaPjQuElco2ddFyQk6KSu7JVMr_IYVJOw0lB-YNs1TMBKi5AMm0rfj817dIVofpD6w4HU9_2c2KZREB3e5q-quInjKSxTlsMwh1xbahLy5xCMpe6293UVwqx7oLQEAc_ldOIbaev9dFBfHz4LqecrPEC2C_OUGg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > 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://secure-web.cisco.com/1wbG0Fxry6mOJBs_6ev8X3E_3JeDZuIS2ENjNzQpbgLx7_AtPaiOUZPpGYm4bt8fjGOpAgf_x4lZoe1U216-cSyJ6KSUvkMellFmQM0uUvxz6_4Nj1m3dTo89tRqnQcifFRWAZhAvGmiMLWQyTR4n1oLXSIw2NMtmiUU-xT8i8HNPExnYqBXz13pwXQAQvIvgO8FHIk7hj8LamRkDOU7TV9HymtoKui0fCtVrzdkSOYOnL-ycBxwqfP6dI7coofSWndjFUtmn3AJT8nMhkwuOww/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > . 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. >
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