External Email - Use Caution
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.siew...@gmx.de>
wrote:
> External Email - Use Caution
>
> 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
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