[Freesurfer] differences in subcortical volumes from version 5.1 to 5.3
Hi, We ran our subjects through version 5.1, did a thorough quality check and troubleshoot the data, and then re-ran our subjects through version 5.3 to verify that our findings were consistent between versions. We're running into an issue where we are not able to replicate our subcortical findings from version 5.1 to 5.3. We did not do a similar quality check and troubleshooting process for the 5.3 data, but did not think that would affect the estimation of the subcortical segmentations. Are there any reasons why these subcortical values would be different between both versions? Thanks, Maia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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.
Re: [Freesurfer] normalization problem (versions 5.1 and 5.3)
Thanks for your response, Bruce. Since we would rather not re-run all 200+ subjects through version 5.3, would it be possible, for the sake of keeping things consistent, to add any flags to recon-all using version 5.1, to be able to include the remaining 35 subjects into our analysis? On Fri, Apr 25, 2014 at 12:49 PM, Maia Pujara maiapuj...@gmail.com wrote: Hi all, After running 200+ subjects through recon-all using version 5.1, all but 30 came back with complete surfaces. The 30 that failed seem to have the same problem with normalization. After re-running these 30 subjects with v5.3, we were able to get a good quality brainmask.mgz output, which was not the case when we ran these subjects through v5.1. See attached for comparisons of v5.1 and v5.3 outputs. Would we need to be adding additional flags to get 5.1 to produce usable results for these subjects? Or might there be some other workaround for this? Thanks in advance! Maia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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.
Re: [Freesurfer] normalization problem (versions 5.1 and 5.3)
To follow up, it makes sense that the noise might be an issue, but it seems like version 5.3 creates the surfaces just fine regardless of the noise, so I'm wondering if perhaps there has been a chance in preprocessing before the end of the T1.mgz computation that solves the problem. Would there happen to be any changes that were made to the normalization step that might be the reason why version 5.1 fails to create complete surfaces for these subjects while version 5.3 is working? Thanks again for your help! On Fri, Apr 25, 2014 at 12:49 PM, Maia Pujara maiapuj...@gmail.com wrote: Hi all, After running 200+ subjects through recon-all using version 5.1, all but 30 came back with complete surfaces. The 30 that failed seem to have the same problem with normalization. After re-running these 30 subjects with v5.3, we were able to get a good quality brainmask.mgz output, which was not the case when we ran these subjects through v5.1. See attached for comparisons of v5.1 and v5.3 outputs. Would we need to be adding additional flags to get 5.1 to produce usable results for these subjects? Or might there be some other workaround for this? Thanks in advance! Maia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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.
