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Is it possible that CAT12 reports volumes after alignment to MNI space (incorrect)?  That is roughly the magnitude of the difference in total brain volume.

 

Matt.

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Michael Mc Laughlin <michael@thecurate.com>
Reply-To: Freesurfer support list <Freesurfer@nmr.mgh.harvard.edu>
Date: Friday, June 9, 2023 at 3:14 AM
To: Freesurfer support list <Freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Huge difference between volumes for Freesurfer vs CAT12

 

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  I have used both CAT12 and Freesurfer to segment a particular brain scan and I get completely different volumes.

 

                              CAT12   Freesurfer 7.3.2
Left Cerebral WM(cc):           209        242
Left Cerebral Cortex (cc)       444        269
Left Lateral Ventricle (cc):     28         43
Right Cerebral WM (cc):         208        242
Right Cerebral Cortex (cc):     440        270
Right Lateral Ventricle (cc):    20         28
----------------------------------------------
Total                          1350       1095

Total brain volume (cc):       1618       1309
Total Intercranial Volume       N/A       1852

 

What could be causing this difference?

 

The brain scan was done with MPRAGE protocol with 176x256x256 voxels of size 1mmx0.976mmx0.976mm

 

Which one is correct?

 

The scan is of a normal adult male aged 62 with chronic migraine.

 

Resent a second time because table did not work well in either of previous attempts

 

 

On Fri, Jun 9, 2023 at 9:00 AM Michael Mc Laughlin <michael@thecurate.com> wrote:

I have used both CAT12 and Freesurfer to segment a particular brain scan and I get completely different volumes.

 

	CAT12 (cc)	Freesurfer 7.3.2 (cc)
Left Cerebral WM(cc):	209	242
Left Cerebral Cortex (cc):	444	269
Left Lateral Ventricle (cc):	28	43
Right Cerebral WM (cc):	208	242
Right Cerebral Cortex (cc):	440	270
Right Lateral Ventricle (cc):	20	28
Total	1350	1095
Total volume (cc):	1618.09	1309
		1852

What could be causing this difference?

 

The brain scan was done with MPRAGE protocol with 176x256x256 voxels of size 1mmx0.976mmx0.976mm

 

Which one is correct?

 

The scan is of a normal adult male aged 62 with chronic migraine.

 

Resent because table did not work well

Michael McLaughlin,

 

On Fri, Jun 9, 2023 at 8:19 AM Michael Mc Laughlin <michael@thecurate.com> wrote:

I have used both CAT12 and Freesurfer to segment a particular brain scan and I get completely different volumes.

 

	CAT12 (cc)		Freesurfer 7.3.2 (cc)
Left Cerebral White Matter volume(cc):	209	Left hemisphere cerebral white matter volume	242
Left Cerebral Cortex volume(cc):	444	Left hemisphere cortical gray matter volume	269
Left Lateral Ventricle volume(cc):	28	Left-Lateral-Ventricle	43
Right Cerebral White Matter volume(cc):	208	Right hemisphere cerebral white matter volume	242
Right Cerebral Cortex volume(cc):	440	Right hemisphere cortical gray matter volume	270
Right Lateral Ventricle volume(cc):	20	Right-Lateral-Ventricle	28
Total	1350	Total	1095
Total volume (cc):	1618.09	Brain Segmentation Volume	1309
		Estimated Total Intracranial Volume	1852

 

What could be causing this difference?

 

The brain scan was done with MPRAGE protocol with 176x256x256 voxels of size 1mmx0.976mmx0.976mm

 

Which one is correct?

 

The scan is of a normal adult male aged 62 with chronic migraine.

Michael McLaughlin,

 

 

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