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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,
External Email - Use Caution
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,
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 7.3.2 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,
External Email - Use Caution
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
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 7.3.2 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.commailto: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.commailto: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,
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
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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,
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1Ybp1V4Lz3tC0E8PpJZJRtdWQ30JABLdG3pR9jvTS339yxR... 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://secure-web.cisco.com/1VyTHLYRGZs_93FJ38kUbv8Bv4k-Qb8oaMwupnpkSDqvW6S... < https://secure-web.cisco.com/1VyTHLYRGZs_93FJ38kUbv8Bv4k-Qb8oaMwupnpkSDqvW6S... . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
freesurfer@nmr.mgh.harvard.edu
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Glasser, Matt -
Michael Mc Laughlin