Hi,

Thanks for the clarification. From my understanding, control points are used to grab regions that should be white matter, rather than remove regions that aren't white matter. Are there any resources on how you would use control points to remove intensity inhomogeneity?

Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Sunday, April 26, 2020 12:03 PM To: Freesurfer support list Subject: [External] Re: [Freesurfer] Intensity inhomogeneity messing with the wm.mgz

Hi Victor

the best way to remove intensity inhomogeneities is with control points usually. The wm.mgz gives us an initial estimate of the surface locations, but we then deform it based on the intensities in the brain.mgz volume. So if it looks like wm extends that far out in the brain your wm.mgz edits are unliekly to fix things

cheers Bruce

On Sun, 26 Apr 2020, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:

Hi Freesurfer developers,

I have a subsample of a FS dataset that have scanner-originated hyperintensities in the bilateral supramarginal/temporal lobes. I've manually removed these hyperintensities by editing the wm.mgz, yet FS seems to be unable to recognize these edits when looking at the ?h.white and aparc+aseg.mgz. Is there a possible way to rectify these errors?

I am using FS6 for linux

Here are some pictures:

[IMAGE]​[IMAGE]

Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

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This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

Hi all,

I was doing a little bit more researching. Could you just fix this sort of issue by editing the aparc.auto.mgz and changing the label from Left/Right-Cerebral-White-Matter to Left/Right-Cerebral-Cortex as necessary?

Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

________________________________________ From: Zeng,Victor (BIDMC - Keshavan - Psychiatry) Sent: Sunday, April 26, 2020 7:28 PM To: Freesurfer support list Subject: Re: [External] Re: [Freesurfer] Intensity inhomogeneity messing with the wm.mgz

Hi,

Thanks for the clarification. From my understanding, control points are used to grab regions that should be white matter, rather than remove regions that aren't white matter. Are there any resources on how you would use control points to remove intensity inhomogeneity?

Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Sunday, April 26, 2020 12:03 PM To: Freesurfer support list Subject: [External] Re: [Freesurfer] Intensity inhomogeneity messing with the wm.mgz

Hi Victor

the best way to remove intensity inhomogeneities is with control points usually. The wm.mgz gives us an initial estimate of the surface locations, but we then deform it based on the intensities in the brain.mgz volume. So if it looks like wm extends that far out in the brain your wm.mgz edits are unliekly to fix things

cheers Bruce

On Sun, 26 Apr 2020, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:

Hi Freesurfer developers,

I have a subsample of a FS dataset that have scanner-originated hyperintensities in the bilateral supramarginal/temporal lobes. I've manually removed these hyperintensities by editing the wm.mgz, yet FS seems to be unable to recognize these edits when looking at the ?h.white and aparc+aseg.mgz. Is there a possible way to rectify these errors?

I am using FS6 for linux

Here are some pictures:

[IMAGE]​[IMAGE]

Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

---

This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

you could I guess, but it will likely be hard, a lot of work, and not that repeatable

cheers Bruce

On Sat, 2 May 2020, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:

Hi all,

I was doing a little bit more researching. Could you just fix this sort of issue by editing the aparc.auto.mgz and changing the label from Left/Right-Cerebral-White-Matter to Left/Right-Cerebral-Cortex as necessary?

Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

---

From: Zeng,Victor (BIDMC - Keshavan - Psychiatry) Sent: Sunday, April 26, 2020 7:28 PM To: Freesurfer support list Subject: Re: [External] Re: [Freesurfer] Intensity inhomogeneity messing with the wm.mgz

Hi,

Thanks for the clarification. From my understanding, control points are used to grab regions that should be white matter, rather than remove regions that aren't white matter. Are there any resources on how you would use control points to remove intensity inhomogeneity?

Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

---

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Sunday, April 26, 2020 12:03 PM To: Freesurfer support list Subject: [External] Re: [Freesurfer] Intensity inhomogeneity messing with the wm.mgz

Hi Victor

the best way to remove intensity inhomogeneities is with control points usually. The wm.mgz gives us an initial estimate of the surface locations, but we then deform it based on the intensities in the brain.mgz volume. So if it looks like wm extends that far out in the brain your wm.mgz edits are unliekly to fix things

cheers Bruce

On Sun, 26 Apr 2020, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:

...

Hi Freesurfer developers,

I have a subsample of a FS dataset that have scanner-originated hyperintensities in the bilateral supramarginal/temporal lobes. I've manually removed these hyperintensities by editing the wm.mgz, yet FS seems to be unable to recognize these edits when looking at the ?h.white and aparc+aseg.mgz. Is there a possible way to rectify these errors?

I am using FS6 for linux

Here are some pictures:

[IMAGE]​[IMAGE]

Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

---

This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

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