External Email - Use Caution
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 <17m...@queensu.ca>
Sent: Monday, January 6, 2020 12:04 PM
To: Tim Schäfer <ts...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Tim Schäfer
<ts...@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?
External Email - Use Caution
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 <17m...@queensu.ca> wrote:
>
>
> External Email - Use Caution
>
> I 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.
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--
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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