Hi Martin, the sample is small (30), and the design is longitudinal, but these structures are not the main focus, which is CT (already manually edited). Thanks for help, Garret
Date: Thu, 24 Sep 2015 14:14:52 -0400 From: [email protected] To: [email protected] Subject: Re: [Freesurfer] segmentation accuracy / aseg edits Hi Garret, again, I am not an editing expert, but some of these look more severe. The question is what you need this for. If this is a population study with 1000 of subjects then obviously editing will be tough. For a small study I would recommend manual edits to make sure you are removing as much noise as possible. Especially if you focus on exactly these structures in your paper. Maybe someone with more editing experience will chime in. Cheers, Martin On 09/24/2015 01:30 PM, Garret O' Connell wrote: Hi Bruce, as you can see in attached image, the hippocampal label (brownish) seems to bleed into 3-4 rows of voxels into a ventrical. In the "amg" image, the amygdala volume (light blue) seems to "wrap" on the outside around the hippocampus a bit, when obviously it should be more spherical. These are the most common errors I find for these respective regions. Within ranges of acceptability? Thanks kindly for help, Garret From: [email protected] Date: Thu, 24 Sep 2015 11:58:18 -0400 To: [email protected] Subject: Re: [Freesurfer] segmentation accuracy / aseg edits Feel free to upload a representative subject and we will take a look Cheers Bruce On Sep 24, 2015, at 11:54 AM, Martin Reuter <[email protected]> wrote: Hi Garret, this is not really a longitudinal question, rather what accuracy can be expected and when do you need to do aseg edits. I therefore changed the title. From what I know, a few voxels here and there will not change the volume measures much. Furthermore, there should be some partial volume correction anyway, so a strong intensity difference should also change the proportional volume. But it would be good if someone with more knowledge about the segmentation details answers. You could edit a single case and see how much difference that makes, I bet it will be small. Best, Martin On 09/24/2015 11:19 AM, Garret O' Connell wrote: Hello FSers, quick question on the validity of FS automatic segmentation. I have found longitudinal changes in hippocampus/amygdala volumes. Upon visual inspection, there are some concerning issues, such as the labelling of CSF in the amygdala. Mostly, these amount to a few clusters of between 5-20 voxels around the boundaries of these structures in around 15-20 % of slices. My question is do these errors sounds abnormally high (and don't think so, having seen examples in some lit about FS accuracy), and are these errors acceptable (publishable with a mild degree of confidence) in the context of a longitudinal design, given the high test-retest reliability of FS segmentation? Or are edits necessary? I know there are probably no right/wrong answers on this, but any advice would be greatly appreciated. Best, Garret _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list [email protected] 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. 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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. _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu _______________________________________________ Freesurfer mailing list [email protected] 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 Partners Compliance HelpLine at http://www.partners.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.
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