External Email - Use Caution
Yes, that must be it. If I calculate the volume of the resulting pial surfaces in the case of CAT12 I get 1080cc and for Freesurfer it is 1154cc which agrees, broadly, with the Freesurfer numbers.
Michael
On Fri, Jun 9, 2023 at 11:41 AM Glasser, Matt glasserm@wustl.edu wrote:
External Email - Use CautionIs 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
External Email - Use Caution *I have used both CAT12 and Freesurfer to segment a particular brain scan
and I get completely different volumes.
CAT12 Freesurfer 7.3.2Left 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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