External Email - Use Caution For skullstrip: recon-all -skullstrip -wsthresh 15 -clean-bm -subjid <insert subject> For wm: recon-all -autorecon2-wm -autorecon3 -subjid <insert subject>
> On Oct 8, 2021, at 12:40 PM, Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > > what were your recon-all commands? > > On 10/2/2021 4:55 PM, Kevin Miller wrote: >> 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/1t6c3QRHyOGeeis2bTOJZieIE6Bbb3C7p5aN-fQs2wL4mbC7E0y8OrzCXL5Drk7mF2uiPVF9jquSJiW8ePACorKzSNaxx1YArpXWvB0leiSLTuFhl_uG_z599fIULMry9v1U1puMg4UwL_na7ERP-oKUjkTZ6JSfV2t7PG3-94AjHvmPYLQqns3CoU4I3MlRBaIoOjv_zINZeHELHxMZ5WfU0xiXr2ekKP3xJ-tgZ-_pUoqg99SvuY2CEGSHvgZHutwJ8iJ7xEzitSXoepP06xA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://secure-web.cisco.com/1t6c3QRHyOGeeis2bTOJZieIE6Bbb3C7p5aN-fQs2wL4mbC7E0y8OrzCXL5Drk7mF2uiPVF9jquSJiW8ePACorKzSNaxx1YArpXWvB0leiSLTuFhl_uG_z599fIULMry9v1U1puMg4UwL_na7ERP-oKUjkTZ6JSfV2t7PG3-94AjHvmPYLQqns3CoU4I3MlRBaIoOjv_zINZeHELHxMZ5WfU0xiXr2ekKP3xJ-tgZ-_pUoqg99SvuY2CEGSHvgZHutwJ8iJ7xEzitSXoepP06xA/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. 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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. >>> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://secure-web.cisco.com/1t6c3QRHyOGeeis2bTOJZieIE6Bbb3C7p5aN-fQs2wL4mbC7E0y8OrzCXL5Drk7mF2uiPVF9jquSJiW8ePACorKzSNaxx1YArpXWvB0leiSLTuFhl_uG_z599fIULMry9v1U1puMg4UwL_na7ERP-oKUjkTZ6JSfV2t7PG3-94AjHvmPYLQqns3CoU4I3MlRBaIoOjv_zINZeHELHxMZ5WfU0xiXr2ekKP3xJ-tgZ-_pUoqg99SvuY2CEGSHvgZHutwJ8iJ7xEzitSXoepP06xA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1t6c3QRHyOGeeis2bTOJZieIE6Bbb3C7p5aN-fQs2wL4mbC7E0y8OrzCXL5Drk7mF2uiPVF9jquSJiW8ePACorKzSNaxx1YArpXWvB0leiSLTuFhl_uG_z599fIULMry9v1U1puMg4UwL_na7ERP-oKUjkTZ6JSfV2t7PG3-94AjHvmPYLQqns3CoU4I3MlRBaIoOjv_zINZeHELHxMZ5WfU0xiXr2ekKP3xJ-tgZ-_pUoqg99SvuY2CEGSHvgZHutwJ8iJ7xEzitSXoepP06xA/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. 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