Thanks for pointing that out. The step numbers are those from section 5 in MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all

On Tue, Aug 30, 2022, 6:16 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

There is not enough information to understand what you did in #2

On 8/30/2022 3:56 PM, Ruifeng Dong wrote:

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Hi all,

I am computing volumetry using freesurfer using two different runs.

1. I just use recon-all -all, and then look at the aseg.stats file.

2. I ran recon-all only to the 12th step where gca labeling is done. It doesn't generate the aseg.mgz file but only aseg.auto.mgz. I assumed that they are the same and ran the -asegstats step to get the output in aseg.stats.

I noticed there are differences between the above two runs on the same image. Firstly, the volumes of WM, GM and ICV are not there from the 2nd run. How does this happen? In which step does Freesurfer compute these?

Secondly, the volumes of some subcortical structures are also different between the two runs. Does Freesurfer make corrections to the volume segmentations after step 12? 

Thank you!

Ruifeng

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