Sorry - made a typo, I meant the aparc.presurfs rather than the aparc.auto.mgz
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --
________________________________________ From: Zeng,Victor (BIDMC - Keshavan - Psychiatry) Sent: Saturday, May 2, 2020 2:58 AM To: Freesurfer support list Subject: Re: [External] Re: [Freesurfer] Intensity inhomogeneity messing with the wm.mgz
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 --
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