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Ah okay, I understand now, thank you very much for the help! In hindsight this was a stupid question. What you said makes things perfectly clear. Thanks again! ________________________________ From: Mohammad Rashid 17mrr6@queensu.ca Sent: Monday, January 6, 2020 12:04 PM To: Tim Schäfer ts+ml@rcmd.org Subject: Re: [Freesurfer] When rerunning recon-all from a later stage, are only edited participants' reconstructions recalculated?
Ah okay, I understand now, thank you very much for the help! In hindsight this was a stupid question. What you said makes things perfectly clear. Thanks again! ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Tim Schäfer ts+ml@rcmd.org Sent: Monday, January 6, 2020 3:29 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] When rerunning recon-all from a later stage, are only edited participants' reconstructions recalculated?
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In your command line:
`recon-all -autorecon2-noaseg -autorecon3 -subjid subj507`
you run the command only for that single subject, 'subj507'. That is exactly what will happen, no command will be run for the other subjects, so their data remains unchanged. It has nothing to do with editing or not.
If you want to run again for other subjects, you would have to run the recon-all command with their subject IDs (one command per subject).
I hope I did not misunderstand your question?
Tim
On January 4, 2020 at 6:09 PM Mohammad Rashid 17mrr6@queensu.ca wrote:
External Email - Use CautionI recently ran this command: `recon-all -autorecon2-noaseg -autorecon3 -subjid subj507` after having edited aseg.mgz (there was too much matter labelled as right hippocampus, so my edit was simply overwriting Right-Hippocampus voxels with Right-Cerebral-White-Matter ones).
After the command's error-free completion, I checked the hippocampal volume measurements of all of the participants again using asegstats2table and found that they were all unchanged, except slight changes to subject subj507's measurements.
So when instructed, does freesurfer only redo the reconstruction and recalculate stats only for those subjects that you've edited? If so, is there a way to have it recalculate every subject, not just those I've edited?
Thank you in advance. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.m...
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
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