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Hi Marie,

Looking at the source code, samseg's sbtiv.stats file sums the volume of the structures listed below. I'm not sure about recon-all's, but I'm assuming it should be similar.

There is indeed no readily-made result for the sum of subcortical structures in samseg, but summing their volumes manually (as you suggest) is indeed the right way to go.

Regarding any discrepancies between recon-all and samseg: these are two quite different methods, so some differences are not unexpected. I think what matters most in your application is to compare volumetry between patient groups *wiithin* each method -- hopefully such differences can be detected reliably no matter which method you use.

Hope this helps,

Koen

'Brain-Stem', 'CSF', 'Left-Cerebellum-Cortex', 'Right-Cerebellum-Cortex', '4th-Ventricle', 'Left-Cerebral-Cortex', 'Right-Cerebral-Cortex', 'Left-Cerebellum-White-Matter', 'Right-Cerebellum-White-Matter', 'Right-Cerebral-White-Matter', 'Left-Cerebral-White-Matter', 'Right-choroid-plexus', 'Right-Amygdala', 'Left-Amygdala', 'Right-Hippocampus', 'Right-Inf-Lat-Vent', 'Left-Hippocampus', 'Left-choroid-plexus', 'Left-Inf-Lat-Vent', 'Optic-Chiasm', 'Right-VentralDC', 'Left-VentralDC', '3rd-Ventricle', 'Left-Accumbens-area', 'Left-Putamen', 'Right-Putamen', 'Right-vessel', 'Right-Accumbens-area', 'WM-hypointensities', 'Left-Lateral-Ventricle', 'Left-vessel', 'Right-Lateral-Ventricle', 'Right-Pallidum', 'Left-Caudate', 'Right-Thalamus', 'Left-Pallidum', 'Right-Caudate', 'Left-Thalamus', 'non-WM-hypointensities', '5th-Ventricle', 'Lesions'

On Mon, Jul 29, 2024 at 2:30 PM Ringki Marie Siewert ringki.siewert@gmx.de wrote:

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Hello Freesurfer Developers,

I'm a medical student using Freesurfer for my PhD. My goal is to measure brain volume and perform brain segmentation of children aged 2-12 years with a leukodystrophy and compare them to controls. I tried both segmentation tools Samseg and recon_all, and now I have some questions about the measurements for I can't find any answers on the wiki pages.

-1. in the sbTIV.stats file created by Samseg the intracranial volume is estimated, however, I don't know wether or not this measurement includes ventricles or to what value of the recon_all aseg.stats file sbTIV.stats corresponds as there are different brain segmentation values.

-2. of what parts constist the total grey matter volume in recon-all? When I sum up cortical grey matter volume and subcortical grey matter volume given in the aseg.stats file the measurement differs from value of total gray matter volume.

-3. of what parts consists the subcortical grey matter volume in recon-all? Samseg measures each structure individually but does not give an overall measurement of subcortical grey matter, is there any way to obtain an overall subcortical measurment via samseg?

-4. last but not least, Samseg and recon-all - even though given the same input file - create very different measurements for cortex volume and overall grey matter volume (using Samseg I simply add up the cortex measurement and each subcortical structure but I'm not sure if that is the right way to go) as well as the volume of ventricles and choroid plexus (using Samseg I add up the volumes of the two lateral ventricles, third ventricle and fourth ventricle as well as the choroid plexus)

I attached the aseg.stats file given by recon-all and the samseg.stats and sbTIV.stats file created running both commands for one person with the same input. I tried many other brain scans but the estimation tendencies stay the same for all of them.

At last I want to thank you for all your hard work! I really appreciate all the advice and support you give.

Have a nice day,

Marie _______________________________________________ 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline < https://www.massgeneralbrigham.org/complianceline%3E .