Re: [Freesurfer] [External] Re: Intensity inhomogeneity messing with the wm.mgz
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-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] [External] Re: Intensity inhomogeneity messing with the wm.mgz
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-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl 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. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] [External] Re: 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-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl 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. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] [External] Re: Intensity inhomogeneity messing with the wm.mgz
Hi Victor control points are used whenever the white matter intensity is incorrect (>>110 or <<110). If you have regions of white matter that are too bright you should be able to put contgrol points in them to bring the region down. For example, if the gm is so bright that it looks like wm, then the nearby white matter should be even brighter cheers Bruce On Sun, 26 Apr 2020, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote: 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-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] [External] Re: 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-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl 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. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
