Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)
Hi Edan
It’s hard for me to see what’s going on in those images. What is the intensity of the white matter in the middle of the occipital strands in the brain.mgz and the brain.finalsurfs.mgz? If it is significantly lower than 110 you probably want some control points in the occipital lobe.
Cheers Bruce
From: Edan Daniel edand@princeton.edu Sent: Friday, February 18, 2022 12:15 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu; Fischl, Bruce BFISCHL@mgh.harvard.edu Subject: Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)
External Email - Use Caution Hi Bruce!
We are focusing on the occipital lobe where the white matter boundary is often too far into the gray matter, and we need those voxels to record visual signals.
Attaching a few images for reference - notice how much 'thicker' the wm segmentation is in the white.preaparc vs the lh.orig.nofix. wm edits of this sort were accepted when we were using the same pipeline with v6 (separate datasets), but now with v7 our edits get 're-corrected' and overwritten. We'd be happy to provide more information or images.
Many thanks!!!
Edan @ PrincetonBrainDevLab
On Thu, Feb 17, 2022 at 7:01 PM Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Edan
Sometimes control points can be more effective than editing the wm, particularly if the intensities in that region are not what we expect (like if the wm and gm are darker than what we try to set them to). Can you post an image or two?
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Edan Daniel Sent: Thursday, February 17, 2022 6:51 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)
External Email - Use Caution
* Different data, same pipeline. In v6 our changes were included in the final white surface segmentation, whereas in v7 they are overwritten during the placement 'refining'. * ?h.orig.nofix and ?h.orig DO reflect edits (?h.orig to some extent). white.preaparc does NOT. * We noticed that the placement is very stubborn and we were not able to overcome this. Methods like manually editing the wm surface worked well with v6 and do not work now with v7. We have also tried editing the filled.mgz with v7.2 following the new tutorial, and that did not work either. Is there any way we can overcome this stubbornness?
Many thanks! Edan @ Princeton BrainDevLab
On Thu, Feb 17, 2022 at 6:07 PM Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> wrote: The edits you are making only change the initial surface; the surface placement then refines the placement. Sometimes the surface placement can be quite stubborn. If this is the case, the ?h.orig.nofix and ?h.orig will reflect your edits (nofix exactly; ?h.orig to some extent). Also check the the white.preaparc is where the problem starts.
When you say that v6 did better, do you mean on this same data or on different data? The surface placement has not changed that much since v6. On 2/14/2022 12:50 PM, Edan Daniel wrote:
External Email - Use Caution We have been having issues with recreating the final surfaces after editing the white matter segmentation, which used to work smoothly in version 6. After running a subject through recon-all (version 7.1.1 *without* the parallel flag) and then editing the white matter, we run the following command (w v7.1.1): recon-all -autorecon2-wm -autorecon3 -subjid ' freesurferfoldername ' -cc-crs ' num2str(corpus_point)
The ribbon file and surfaces do update *very slightly* but it’s largely ignoring our (sometimes large) edits. This pipeline worked well for us in version 6- do you have any idea what might be going on?
Would love to hear your thoughts about this.
Many thanks!! Edan, Braindevlab@Princeton
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Thanks Bruce! This looks like a helpful solution for the places where the wm is not identified- we will definitely try it! We have one other type of issue which is more prevalent, that I was not sure if control points will be able to help with (we have not worked with control points before so sorry if this is a misinformed question) The main issue we're facing is that the final segmentation we get is too aggressive, that is, in many places too *many* voxels are categorized as wm and thus we have lower ability to characterize properties of the gray matter in the occipital cortex. What we usually do is clean the wm segmentation to make it less bulky, but now these edits are not being incorporated in the final segmentation. We are very confused by this because this type of edits were easily incorporated in v6, but not with v7. From my understanding- the control points would be helpful in the opposite case- where not enough voxels are recognized as wm (such as in the rightmost part of the attached image)- but not much in the rest of the image where we can see that the magenta borders (x.orig.nofix) are 'tighter' around the wm when compared to the borders after running through recon -wm (teal, x.white.preaparc). Is there a way to leverage the control points for this cause, or is there something else we can try to make the recon -wm less stubborn and accept our manual edits?
For reference, the full command we run is as follows:
recon-all -autorecon2-wm -autorecon3 -subjid ' freesurferfoldername ' -cc-crs ' num2str(corpus_point)
Attaching another image - please let me know if the visibility here is better or if you'd like to see a different visualization.
Many thanks!!!! Edan @ PrincetonBrainDevLab
On Fri, Feb 18, 2022 at 9:53 AM Fischl, Bruce BFISCHL@mgh.harvard.edu wrote:
Hi Edan
It’s hard for me to see what’s going on in those images. What is the intensity of the white matter in the middle of the occipital strands in the brain.mgz and the brain.finalsurfs.mgz? If it is significantly lower than 110 you probably want some control points in the occipital lobe.
Cheers Bruce
*From:* Edan Daniel edand@princeton.edu *Sent:* Friday, February 18, 2022 12:15 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu; Fischl, Bruce BFISCHL@mgh.harvard.edu *Subject:* Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)
External Email - Use Caution *Hi Bruce!
We are focusing on the occipital lobe where the white matter boundary is often too far into the gray matter, and we need those voxels to record visual signals.
Attaching a few images for reference - notice how much 'thicker' the wm segmentation is in the white.preaparc vs the lh.orig.nofix. wm edits of this sort were accepted when we were using the same pipeline with v6 (separate datasets), but now with v7 our edits get 're-corrected' and overwritten. We'd be happy to provide more information or images.
Many thanks!!!
Edan @ PrincetonBrainDevLab
On Thu, Feb 17, 2022 at 7:01 PM Fischl, Bruce BFISCHL@mgh.harvard.edu wrote:
Hi Edan
Sometimes control points can be more effective than editing the wm, particularly if the intensities in that region are not what we expect (like if the wm and gm are darker than what we try to set them to). Can you post an image or two?
Cheers
Bruce
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Edan Daniel *Sent:* Thursday, February 17, 2022 6:51 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)
External Email - Use Caution *
- Different data, same pipeline. In v6 our changes were included in
the final white surface segmentation, whereas in v7 they are overwritten during the placement 'refining'.
- ?h.orig.nofix and ?h.orig DO reflect edits (?h.orig to some extent).
white.preaparc does NOT.
- We noticed that the placement is very stubborn and we were not able
to overcome this. Methods like manually editing the wm surface worked well with v6 and do not work now with v7. We have also tried editing the filled.mgz with v7.2 following the new tutorial, and that did not work either.
Is there any way we can overcome this stubbornness?
Many thanks!
Edan @ Princeton BrainDevLab
On Thu, Feb 17, 2022 at 6:07 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
The edits you are making only change the initial surface; the surface placement then refines the placement. Sometimes the surface placement can be quite stubborn. If this is the case, the ?h.orig.nofix and ?h.orig will reflect your edits (nofix exactly; ?h.orig to some extent). Also check the the white.preaparc is where the problem starts.
When you say that v6 did better, do you mean on this same data or on different data? The surface placement has not changed that much since v6.
On 2/14/2022 12:50 PM, Edan Daniel wrote:
External Email - Use Caution *We have been having issues with recreating the final surfaces after editing the white matter segmentation, which used to work smoothly in version 6. After running a subject through recon-all (version 7.1.1 *without* the parallel flag) and then editing the white matter, we run the following command (w v7.1.1):
recon-all -autorecon2-wm -autorecon3 -subjid ' freesurferfoldername ' -cc-crs ' num2str(corpus_point)
The ribbon file and surfaces do update *very slightly* but it’s largely ignoring our (sometimes large) edits. This pipeline worked well for us in version 6- do you have any idea what might be going on?
Would love to hear your thoughts about this.
Many thanks!!
Edan, Braindevlab@Princeton
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Hi Edan
Control points might be helpful in both cases, but you are right it is more often the case when the wm is too dark. Another thing you can try is using expert options for mri_segment to constrain the intensity ranges of wm/gm. Or you could try using the samseg stream (someone else will have to help you with this, but it might well do better for your acquisitions)
Cheers Bruce
From: Edan Daniel edand@princeton.edu Sent: Monday, February 21, 2022 11:14 AM To: Fischl, Bruce BFISCHL@mgh.harvard.edu Cc: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)
External Email - Use Caution Thanks Bruce! This looks like a helpful solution for the places where the wm is not identified- we will definitely try it! We have one other type of issue which is more prevalent, that I was not sure if control points will be able to help with (we have not worked with control points before so sorry if this is a misinformed question) The main issue we're facing is that the final segmentation we get is too aggressive, that is, in many places too *many* voxels are categorized as wm and thus we have lower ability to characterize properties of the gray matter in the occipital cortex. What we usually do is clean the wm segmentation to make it less bulky, but now these edits are not being incorporated in the final segmentation. We are very confused by this because this type of edits were easily incorporated in v6, but not with v7. From my understanding- the control points would be helpful in the opposite case- where not enough voxels are recognized as wm (such as in the rightmost part of the attached image)- but not much in the rest of the image where we can see that the magenta borders (x.orig.nofix) are 'tighter' around the wm when compared to the borders after running through recon -wm (teal, x.white.preaparc). Is there a way to leverage the control points for this cause, or is there something else we can try to make the recon -wm less stubborn and accept our manual edits?
For reference, the full command we run is as follows: recon-all -autorecon2-wm -autorecon3 -subjid ' freesurferfoldername ' -cc-crs ' num2str(corpus_point)
Attaching another image - please let me know if the visibility here is better or if you'd like to see a different visualization.
Many thanks!!!! Edan @ PrincetonBrainDevLab
On Fri, Feb 18, 2022 at 9:53 AM Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Edan
It’s hard for me to see what’s going on in those images. What is the intensity of the white matter in the middle of the occipital strands in the brain.mgz and the brain.finalsurfs.mgz? If it is significantly lower than 110 you probably want some control points in the occipital lobe.
Cheers Bruce
From: Edan Daniel <edand@princeton.edumailto:edand@princeton.edu> Sent: Friday, February 18, 2022 12:15 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>; Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Subject: Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)
External Email - Use Caution Hi Bruce!
We are focusing on the occipital lobe where the white matter boundary is often too far into the gray matter, and we need those voxels to record visual signals.
Attaching a few images for reference - notice how much 'thicker' the wm segmentation is in the white.preaparc vs the lh.orig.nofix. wm edits of this sort were accepted when we were using the same pipeline with v6 (separate datasets), but now with v7 our edits get 're-corrected' and overwritten. We'd be happy to provide more information or images.
Many thanks!!!
Edan @ PrincetonBrainDevLab
On Thu, Feb 17, 2022 at 7:01 PM Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Edan
Sometimes control points can be more effective than editing the wm, particularly if the intensities in that region are not what we expect (like if the wm and gm are darker than what we try to set them to). Can you post an image or two?
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Edan Daniel Sent: Thursday, February 17, 2022 6:51 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)
External Email - Use Caution
* Different data, same pipeline. In v6 our changes were included in the final white surface segmentation, whereas in v7 they are overwritten during the placement 'refining'. * ?h.orig.nofix and ?h.orig DO reflect edits (?h.orig to some extent). white.preaparc does NOT. * We noticed that the placement is very stubborn and we were not able to overcome this. Methods like manually editing the wm surface worked well with v6 and do not work now with v7. We have also tried editing the filled.mgz with v7.2 following the new tutorial, and that did not work either. Is there any way we can overcome this stubbornness?
Many thanks! Edan @ Princeton BrainDevLab
On Thu, Feb 17, 2022 at 6:07 PM Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> wrote: The edits you are making only change the initial surface; the surface placement then refines the placement. Sometimes the surface placement can be quite stubborn. If this is the case, the ?h.orig.nofix and ?h.orig will reflect your edits (nofix exactly; ?h.orig to some extent). Also check the the white.preaparc is where the problem starts.
When you say that v6 did better, do you mean on this same data or on different data? The surface placement has not changed that much since v6. On 2/14/2022 12:50 PM, Edan Daniel wrote:
External Email - Use Caution We have been having issues with recreating the final surfaces after editing the white matter segmentation, which used to work smoothly in version 6. After running a subject through recon-all (version 7.1.1 *without* the parallel flag) and then editing the white matter, we run the following command (w v7.1.1): recon-all -autorecon2-wm -autorecon3 -subjid ' freesurferfoldername ' -cc-crs ' num2str(corpus_point)
The ribbon file and surfaces do update *very slightly* but it’s largely ignoring our (sometimes large) edits. This pipeline worked well for us in version 6- do you have any idea what might be going on?
Would love to hear your thoughts about this.
Many thanks!! Edan, Braindevlab@Princeton
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If this is not something you have to do a lot of, you can put a repositioning point. See the release notes.
On 2/21/2022 1:10 PM, Fischl, Bruce wrote:
Hi Edan
Control points might be helpful in both cases, but you are right it is more often the case when the wm is too dark. Another thing you can try is using expert options for mri_segment to constrain the intensity ranges of wm/gm. Or you could try using the samseg stream (someone else will have to help you with this, but it might well do better for your acquisitions)
Cheers
Bruce
*From:* Edan Daniel edand@princeton.edu *Sent:* Monday, February 21, 2022 11:14 AM *To:* Fischl, Bruce BFISCHL@mgh.harvard.edu *Cc:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)
* External Email - Use Caution *
Thanks Bruce!
This looks like a helpful solution for the places where the wm is not identified- we will definitely try it!
We have one other type of issue which is more prevalent, that I was not sure if control points will be able to help with (we have not worked with control points before so sorry if this is a misinformed question)
The main issue we're facing is that the final segmentation we get is too aggressive, that is, in many places too *many* voxels are categorized as wm and thus we have lower ability to characterize properties of the gray matter in the occipital cortex. What we usually do is clean the wm segmentation to make it less bulky, but now these edits are not being incorporated in the final segmentation. We are very confused by this because this type of edits were easily incorporated in v6, but not with v7.
From my understanding- the control points would be helpful in the opposite case- where not enough voxels are recognized as wm (such as in the rightmost part of the attached image)- but not much in the rest of the image where we can see that the magenta borders (x.orig.nofix) are 'tighter' around the wm when compared to the borders after running through recon -wm (teal, x.white.preaparc).
Is there a way to leverage the control points for this cause, or is there something else we can try to make the recon -wm less stubborn and accept our manual edits?
For reference, the full command we run is as follows:
recon-all -autorecon2-wm -autorecon3 -subjid ' freesurferfoldername ' -cc-crs ' num2str(corpus_point)Attaching another image - please let me know if the visibility here is better or if you'd like to see a different visualization.
Many thanks!!!!
Edan @ PrincetonBrainDevLab
On Fri, Feb 18, 2022 at 9:53 AM Fischl, Bruce BFISCHL@mgh.harvard.edu wrote:
Hi Edan It’s hard for me to see what’s going on in those images. What is the intensity of the white matter in the middle of the occipital strands in the brain.mgz and the brain.finalsurfs.mgz? If it is significantly lower than 110 you probably want some control points in the occipital lobe. Cheers Bruce *From:* Edan Daniel <edand@princeton.edu> *Sent:* Friday, February 18, 2022 12:15 AM *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; Fischl, Bruce <BFISCHL@mgh.harvard.edu> *Subject:* Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0) * External Email - Use Caution * Hi Bruce! We are focusing on the occipital lobe where the white matter boundary is often too far into the gray matter, and we need those voxels to record visual signals. Attaching a few images for reference - notice how much 'thicker' the wm segmentation is in the white.preaparc vs the lh.orig.nofix. wm edits of this sort were accepted when we were using the same pipeline with v6 (separate datasets), but now with v7 our edits get 're-corrected' and overwritten. We'd be happy to provide more information or images. Many thanks!!! Edan @ PrincetonBrainDevLab On Thu, Feb 17, 2022 at 7:01 PM Fischl, Bruce <BFISCHL@mgh.harvard.edu> wrote: Hi Edan Sometimes control points can be more effective than editing the wm, particularly if the intensities in that region are not what we expect (like if the wm and gm are darker than what we try to set them to). Can you post an image or two? Cheers Bruce *From:* freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Edan Daniel *Sent:* Thursday, February 17, 2022 6:51 PM *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> *Subject:* Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0) * External Email - Use Caution * * Different data, same pipeline. In v6 our changes were included in the final white surface segmentation, whereas in v7 they are overwritten during the placement 'refining'. * ?h.orig.nofix and ?h.orig DO reflect edits (?h.orig to some extent). white.preaparc does NOT. * We noticed that the placement is very stubborn and we were not able to overcome this. Methods like manually editing the wm surface worked well with v6 and do not work now with v7. We have also tried editing the filled.mgz with v7.2 following the new tutorial, and that did not work either. Is there any way we can overcome this stubbornness? Many thanks! Edan @ Princeton BrainDevLab On Thu, Feb 17, 2022 at 6:07 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote: The edits you are making only change the initial surface; the surface placement then refines the placement. Sometimes the surface placement can be quite stubborn. If this is the case, the ?h.orig.nofix and ?h.orig will reflect your edits (nofix exactly; ?h.orig to some extent). Also check the the white.preaparc is where the problem starts. When you say that v6 did better, do you mean on this same data or on different data? The surface placement has not changed that much since v6. On 2/14/2022 12:50 PM, Edan Daniel wrote: * External Email - Use Caution * We have been having issues with recreating the final surfaces after editing the white matter segmentation, which used to work smoothly in version 6. After running a subject through recon-all (version 7.1.1 *without* the parallel flag) and then editing the white matter, we run the following command (w v7.1.1): recon-all -autorecon2-wm -autorecon3 -subjid ' freesurferfoldername ' -cc-crs ' num2str(corpus_point) The ribbon file and surfaces do update *very slightly* but it’s largely ignoring our (sometimes large) edits. This pipeline worked well for us in version 6- do you have any idea what might be going on? Would love to hear your thoughts about this. Many thanks!! Edan, Braindevlab@Princeton _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1BhcjfvnDAXHKeDR6R-iodPMLY3xi6xzTIkDcLTzdfO3AL026S0Y3nNiwNsk_Rhlx_6JzCATRItAPsiC_YL1qTPC76JQ1MNnw3UFSezKkrQcBMfyG1DRPHx23o0SxD83e-UdoqRq6N_xTPo7NheFjY7DCWEVDO0VG4JQcj_B6gRwgTjcEusrZjCc7AIQLTBCPjUGmV7iAA6k3S4pAbv0fOyoEPiRWC2ZgYRUgdQU37hKnQcsQQh0NXPeMNjg9XNO503u9KpbREhWN6C_FpIcwAg0QwUJZtmVUfCQCbYUiXIzPMh5ccArQBCnw4ESKv_GujZUYT0Xdb3SffsHy_AhtuA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1BhcjfvnDAXHKeDR6R-iodPMLY3xi6xzTIkDcLTzdfO3AL026S0Y3nNiwNsk_Rhlx_6JzCATRItAPsiC_YL1qTPC76JQ1MNnw3UFSezKkrQcBMfyG1DRPHx23o0SxD83e-UdoqRq6N_xTPo7NheFjY7DCWEVDO0VG4JQcj_B6gRwgTjcEusrZjCc7AIQLTBCPjUGmV7iAA6k3S4pAbv0fOyoEPiRWC2ZgYRUgdQU37hKnQcsQQh0NXPeMNjg9XNO503u9KpbREhWN6C_FpIcwAg0QwUJZtmVUfCQCbYUiXIzPMh5ccArQBCnw4ESKv_GujZUYT0Xdb3SffsHy_AhtuA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/12WGi9fwMNRKoc7g0UsFngq4QzxkPkp8uUBbbPuKzCH_q-TezGLWNd9gLzSp5bA5xyVBH4b49Ud7EB5J4_56yDSUeCG8y4c9zwEkJDUAc0Twj6u13EwndIb9BDN6wtlLMFHjG8bvBBhNl4Eku3J-b3JAibe2gc0BJQdXG3SDNjvzjTedpGREZ5R1OxhDqNatpoOWUkC7c7gNubVq8xP8-ifLLMnnaz-Y8YMsLkKNy6MZTu8U3DuMberr-t84pfbtBdl4XlvA_HRz0s2rMYnsl2DHweu8kDVysoXaKUBeUYf9RBeRHtRniA7Bv98iG7P9a/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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Hi Doug, It is something we do *a lot* of, thus we hoped we'd be able to find a way to make the recon-wm implement our edits without additional manual edits, like we used to do with v6. Do you have any idea what could have caused this change in stubbornness in v7, or how would it be best to try to overcome this? We can try using the samseg stream as Bruce has kindly suggested, but we hoped to find a way to make our standard fs pipeline work with v7.
Many thanks!!! Edan @ PrincetonBrainDevLab
On Mon, Feb 21, 2022 at 5:04 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
If this is not something you have to do a lot of, you can put a repositioning point. See the release notes.
On 2/21/2022 1:10 PM, Fischl, Bruce wrote:
Hi Edan
Control points might be helpful in both cases, but you are right it is more often the case when the wm is too dark. Another thing you can try is using expert options for mri_segment to constrain the intensity ranges of wm/gm. Or you could try using the samseg stream (someone else will have to help you with this, but it might well do better for your acquisitions)
Cheers
Bruce
*From:* Edan Daniel edand@princeton.edu edand@princeton.edu *Sent:* Monday, February 21, 2022 11:14 AM *To:* Fischl, Bruce BFISCHL@mgh.harvard.edu BFISCHL@mgh.harvard.edu *Cc:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)
External Email - Use Caution *Thanks Bruce!
This looks like a helpful solution for the places where the wm is not identified- we will definitely try it!
We have one other type of issue which is more prevalent, that I was not sure if control points will be able to help with (we have not worked with control points before so sorry if this is a misinformed question)
The main issue we're facing is that the final segmentation we get is too aggressive, that is, in many places too *many* voxels are categorized as wm and thus we have lower ability to characterize properties of the gray matter in the occipital cortex. What we usually do is clean the wm segmentation to make it less bulky, but now these edits are not being incorporated in the final segmentation. We are very confused by this because this type of edits were easily incorporated in v6, but not with v7.
From my understanding- the control points would be helpful in the opposite case- where not enough voxels are recognized as wm (such as in the rightmost part of the attached image)- but not much in the rest of the image where we can see that the magenta borders (x.orig.nofix) are 'tighter' around the wm when compared to the borders after running through recon -wm (teal, x.white.preaparc).
Is there a way to leverage the control points for this cause, or is there something else we can try to make the recon -wm less stubborn and accept our manual edits?
For reference, the full command we run is as follows:
recon-all -autorecon2-wm -autorecon3 -subjid ' freesurferfoldername ' -cc-crs ' num2str(corpus_point)
Attaching another image - please let me know if the visibility here is better or if you'd like to see a different visualization.
Many thanks!!!!
Edan @ PrincetonBrainDevLab
On Fri, Feb 18, 2022 at 9:53 AM Fischl, Bruce BFISCHL@mgh.harvard.edu wrote:
Hi Edan
It’s hard for me to see what’s going on in those images. What is the intensity of the white matter in the middle of the occipital strands in the brain.mgz and the brain.finalsurfs.mgz? If it is significantly lower than 110 you probably want some control points in the occipital lobe.
Cheers Bruce
*From:* Edan Daniel edand@princeton.edu *Sent:* Friday, February 18, 2022 12:15 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu; Fischl, Bruce BFISCHL@mgh.harvard.edu *Subject:* Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)
External Email - Use Caution *Hi Bruce!
We are focusing on the occipital lobe where the white matter boundary is often too far into the gray matter, and we need those voxels to record visual signals.
Attaching a few images for reference - notice how much 'thicker' the wm segmentation is in the white.preaparc vs the lh.orig.nofix. wm edits of this sort were accepted when we were using the same pipeline with v6 (separate datasets), but now with v7 our edits get 're-corrected' and overwritten. We'd be happy to provide more information or images.
Many thanks!!!
Edan @ PrincetonBrainDevLab
On Thu, Feb 17, 2022 at 7:01 PM Fischl, Bruce BFISCHL@mgh.harvard.edu wrote:
Hi Edan
Sometimes control points can be more effective than editing the wm, particularly if the intensities in that region are not what we expect (like if the wm and gm are darker than what we try to set them to). Can you post an image or two?
Cheers
Bruce
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Edan Daniel *Sent:* Thursday, February 17, 2022 6:51 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)
External Email - Use Caution *
- Different data, same pipeline. In v6 our changes were included in
the final white surface segmentation, whereas in v7 they are overwritten during the placement 'refining'.
- ?h.orig.nofix and ?h.orig DO reflect edits (?h.orig to some extent).
white.preaparc does NOT.
- We noticed that the placement is very stubborn and we were not able
to overcome this. Methods like manually editing the wm surface worked well with v6 and do not work now with v7. We have also tried editing the filled.mgz with v7.2 following the new tutorial, and that did not work either.
Is there any way we can overcome this stubbornness?
Many thanks!
Edan @ Princeton BrainDevLab
On Thu, Feb 17, 2022 at 6:07 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
The edits you are making only change the initial surface; the surface placement then refines the placement. Sometimes the surface placement can be quite stubborn. If this is the case, the ?h.orig.nofix and ?h.orig will reflect your edits (nofix exactly; ?h.orig to some extent). Also check the the white.preaparc is where the problem starts.
When you say that v6 did better, do you mean on this same data or on different data? The surface placement has not changed that much since v6.
On 2/14/2022 12:50 PM, Edan Daniel wrote:
External Email - Use Caution *We have been having issues with recreating the final surfaces after editing the white matter segmentation, which used to work smoothly in version 6. After running a subject through recon-all (version 7.1.1 *without* the parallel flag) and then editing the white matter, we run the following command (w v7.1.1):
recon-all -autorecon2-wm -autorecon3 -subjid ' freesurferfoldername ' -cc-crs ' num2str(corpus_point)
The ribbon file and surfaces do update *very slightly* but it’s largely ignoring our (sometimes large) edits. This pipeline worked well for us in version 6- do you have any idea what might be going on?
Would love to hear your thoughts about this.
Many thanks!!
Edan, Braindevlab@Princeton
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I think your best bet is either samseg or try expert options to tune mri_segment and/or mris_make_surfaces
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Edan Daniel Sent: Monday, February 21, 2022 6:30 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu; Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Subject: Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)
External Email - Use Caution Hi Doug, It is something we do *a lot* of, thus we hoped we'd be able to find a way to make the recon-wm implement our edits without additional manual edits, like we used to do with v6. Do you have any idea what could have caused this change in stubbornness in v7, or how would it be best to try to overcome this? We can try using the samseg stream as Bruce has kindly suggested, but we hoped to find a way to make our standard fs pipeline work with v7.
Many thanks!!! Edan @ PrincetonBrainDevLab
On Mon, Feb 21, 2022 at 5:04 PM Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> wrote: If this is not something you have to do a lot of, you can put a repositioning point. See the release notes. On 2/21/2022 1:10 PM, Fischl, Bruce wrote: Hi Edan
Control points might be helpful in both cases, but you are right it is more often the case when the wm is too dark. Another thing you can try is using expert options for mri_segment to constrain the intensity ranges of wm/gm. Or you could try using the samseg stream (someone else will have to help you with this, but it might well do better for your acquisitions)
Cheers Bruce
From: Edan Daniel edand@princeton.edumailto:edand@princeton.edu Sent: Monday, February 21, 2022 11:14 AM To: Fischl, Bruce BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu Cc: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)
External Email - Use Caution Thanks Bruce! This looks like a helpful solution for the places where the wm is not identified- we will definitely try it! We have one other type of issue which is more prevalent, that I was not sure if control points will be able to help with (we have not worked with control points before so sorry if this is a misinformed question) The main issue we're facing is that the final segmentation we get is too aggressive, that is, in many places too *many* voxels are categorized as wm and thus we have lower ability to characterize properties of the gray matter in the occipital cortex. What we usually do is clean the wm segmentation to make it less bulky, but now these edits are not being incorporated in the final segmentation. We are very confused by this because this type of edits were easily incorporated in v6, but not with v7. From my understanding- the control points would be helpful in the opposite case- where not enough voxels are recognized as wm (such as in the rightmost part of the attached image)- but not much in the rest of the image where we can see that the magenta borders (x.orig.nofix) are 'tighter' around the wm when compared to the borders after running through recon -wm (teal, x.white.preaparc). Is there a way to leverage the control points for this cause, or is there something else we can try to make the recon -wm less stubborn and accept our manual edits?
For reference, the full command we run is as follows: recon-all -autorecon2-wm -autorecon3 -subjid ' freesurferfoldername ' -cc-crs ' num2str(corpus_point)
Attaching another image - please let me know if the visibility here is better or if you'd like to see a different visualization.
Many thanks!!!! Edan @ PrincetonBrainDevLab
On Fri, Feb 18, 2022 at 9:53 AM Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Edan
It’s hard for me to see what’s going on in those images. What is the intensity of the white matter in the middle of the occipital strands in the brain.mgz and the brain.finalsurfs.mgz? If it is significantly lower than 110 you probably want some control points in the occipital lobe.
Cheers Bruce
From: Edan Daniel <edand@princeton.edumailto:edand@princeton.edu> Sent: Friday, February 18, 2022 12:15 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>; Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Subject: Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)
External Email - Use Caution Hi Bruce!
We are focusing on the occipital lobe where the white matter boundary is often too far into the gray matter, and we need those voxels to record visual signals.
Attaching a few images for reference - notice how much 'thicker' the wm segmentation is in the white.preaparc vs the lh.orig.nofix. wm edits of this sort were accepted when we were using the same pipeline with v6 (separate datasets), but now with v7 our edits get 're-corrected' and overwritten. We'd be happy to provide more information or images.
Many thanks!!!
Edan @ PrincetonBrainDevLab
On Thu, Feb 17, 2022 at 7:01 PM Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Edan
Sometimes control points can be more effective than editing the wm, particularly if the intensities in that region are not what we expect (like if the wm and gm are darker than what we try to set them to). Can you post an image or two?
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Edan Daniel Sent: Thursday, February 17, 2022 6:51 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)
External Email - Use Caution
* Different data, same pipeline. In v6 our changes were included in the final white surface segmentation, whereas in v7 they are overwritten during the placement 'refining'. * ?h.orig.nofix and ?h.orig DO reflect edits (?h.orig to some extent). white.preaparc does NOT. * We noticed that the placement is very stubborn and we were not able to overcome this. Methods like manually editing the wm surface worked well with v6 and do not work now with v7. We have also tried editing the filled.mgz with v7.2 following the new tutorial, and that did not work either. Is there any way we can overcome this stubbornness?
Many thanks! Edan @ Princeton BrainDevLab
On Thu, Feb 17, 2022 at 6:07 PM Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> wrote: The edits you are making only change the initial surface; the surface placement then refines the placement. Sometimes the surface placement can be quite stubborn. If this is the case, the ?h.orig.nofix and ?h.orig will reflect your edits (nofix exactly; ?h.orig to some extent). Also check the the white.preaparc is where the problem starts.
When you say that v6 did better, do you mean on this same data or on different data? The surface placement has not changed that much since v6. On 2/14/2022 12:50 PM, Edan Daniel wrote:
External Email - Use Caution We have been having issues with recreating the final surfaces after editing the white matter segmentation, which used to work smoothly in version 6. After running a subject through recon-all (version 7.1.1 *without* the parallel flag) and then editing the white matter, we run the following command (w v7.1.1): recon-all -autorecon2-wm -autorecon3 -subjid ' freesurferfoldername ' -cc-crs ' num2str(corpus_point)
The ribbon file and surfaces do update *very slightly* but it’s largely ignoring our (sometimes large) edits. This pipeline worked well for us in version 6- do you have any idea what might be going on?
Would love to hear your thoughts about this.
Many thanks!! Edan, Braindevlab@Princeton
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External Email - Use Caution
Thanks!
On Mon, Feb 21, 2022 at 6:42 PM Fischl, Bruce BFISCHL@mgh.harvard.edu wrote:
I think your best bet is either samseg or try expert options to tune mri_segment and/or mris_make_surfaces
Cheers
Bruce
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Edan Daniel *Sent:* Monday, February 21, 2022 6:30 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu; Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Subject:* Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)
External Email - Use Caution *Hi Doug,
It is something we do *a lot* of, thus we hoped we'd be able to find a way to make the recon-wm implement our edits without additional manual edits, like we used to do with v6.
Do you have any idea what could have caused this change in stubbornness in v7, or how would it be best to try to overcome this?
We can try using the samseg stream as Bruce has kindly suggested, but we hoped to find a way to make our standard fs pipeline work with v7.
Many thanks!!!
Edan @ PrincetonBrainDevLab
On Mon, Feb 21, 2022 at 5:04 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
If this is not something you have to do a lot of, you can put a repositioning point. See the release notes.
On 2/21/2022 1:10 PM, Fischl, Bruce wrote:
Hi Edan
Control points might be helpful in both cases, but you are right it is more often the case when the wm is too dark. Another thing you can try is using expert options for mri_segment to constrain the intensity ranges of wm/gm. Or you could try using the samseg stream (someone else will have to help you with this, but it might well do better for your acquisitions)
Cheers
Bruce
*From:* Edan Daniel edand@princeton.edu edand@princeton.edu *Sent:* Monday, February 21, 2022 11:14 AM *To:* Fischl, Bruce BFISCHL@mgh.harvard.edu BFISCHL@mgh.harvard.edu *Cc:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)
External Email - Use Caution *Thanks Bruce!
This looks like a helpful solution for the places where the wm is not identified- we will definitely try it!
We have one other type of issue which is more prevalent, that I was not sure if control points will be able to help with (we have not worked with control points before so sorry if this is a misinformed question)
The main issue we're facing is that the final segmentation we get is too aggressive, that is, in many places too *many* voxels are categorized as wm and thus we have lower ability to characterize properties of the gray matter in the occipital cortex. What we usually do is clean the wm segmentation to make it less bulky, but now these edits are not being incorporated in the final segmentation. We are very confused by this because this type of edits were easily incorporated in v6, but not with v7.
From my understanding- the control points would be helpful in the opposite case- where not enough voxels are recognized as wm (such as in the rightmost part of the attached image)- but not much in the rest of the image where we can see that the magenta borders (x.orig.nofix) are 'tighter' around the wm when compared to the borders after running through recon -wm (teal, x.white.preaparc).
Is there a way to leverage the control points for this cause, or is there something else we can try to make the recon -wm less stubborn and accept our manual edits?
For reference, the full command we run is as follows:
recon-all -autorecon2-wm -autorecon3 -subjid ' freesurferfoldername ' -cc-crs ' num2str(corpus_point)
Attaching another image - please let me know if the visibility here is better or if you'd like to see a different visualization.
Many thanks!!!!
Edan @ PrincetonBrainDevLab
On Fri, Feb 18, 2022 at 9:53 AM Fischl, Bruce BFISCHL@mgh.harvard.edu wrote:
Hi Edan
It’s hard for me to see what’s going on in those images. What is the intensity of the white matter in the middle of the occipital strands in the brain.mgz and the brain.finalsurfs.mgz? If it is significantly lower than 110 you probably want some control points in the occipital lobe.
Cheers Bruce
*From:* Edan Daniel edand@princeton.edu *Sent:* Friday, February 18, 2022 12:15 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu; Fischl, Bruce BFISCHL@mgh.harvard.edu *Subject:* Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)
External Email - Use Caution *Hi Bruce!
We are focusing on the occipital lobe where the white matter boundary is often too far into the gray matter, and we need those voxels to record visual signals.
Attaching a few images for reference - notice how much 'thicker' the wm segmentation is in the white.preaparc vs the lh.orig.nofix. wm edits of this sort were accepted when we were using the same pipeline with v6 (separate datasets), but now with v7 our edits get 're-corrected' and overwritten. We'd be happy to provide more information or images.
Many thanks!!!
Edan @ PrincetonBrainDevLab
On Thu, Feb 17, 2022 at 7:01 PM Fischl, Bruce BFISCHL@mgh.harvard.edu wrote:
Hi Edan
Sometimes control points can be more effective than editing the wm, particularly if the intensities in that region are not what we expect (like if the wm and gm are darker than what we try to set them to). Can you post an image or two?
Cheers
Bruce
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Edan Daniel *Sent:* Thursday, February 17, 2022 6:51 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)
External Email - Use Caution *
- Different data, same pipeline. In v6 our changes were included in
the final white surface segmentation, whereas in v7 they are overwritten during the placement 'refining'.
- ?h.orig.nofix and ?h.orig DO reflect edits (?h.orig to some extent).
white.preaparc does NOT.
- We noticed that the placement is very stubborn and we were not able
to overcome this. Methods like manually editing the wm surface worked well with v6 and do not work now with v7. We have also tried editing the filled.mgz with v7.2 following the new tutorial, and that did not work either.
Is there any way we can overcome this stubbornness?
Many thanks!
Edan @ Princeton BrainDevLab
On Thu, Feb 17, 2022 at 6:07 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
The edits you are making only change the initial surface; the surface placement then refines the placement. Sometimes the surface placement can be quite stubborn. If this is the case, the ?h.orig.nofix and ?h.orig will reflect your edits (nofix exactly; ?h.orig to some extent). Also check the the white.preaparc is where the problem starts.
When you say that v6 did better, do you mean on this same data or on different data? The surface placement has not changed that much since v6.
On 2/14/2022 12:50 PM, Edan Daniel wrote:
External Email - Use Caution *We have been having issues with recreating the final surfaces after editing the white matter segmentation, which used to work smoothly in version 6. After running a subject through recon-all (version 7.1.1 *without* the parallel flag) and then editing the white matter, we run the following command (w v7.1.1):
recon-all -autorecon2-wm -autorecon3 -subjid ' freesurferfoldername ' -cc-crs ' num2str(corpus_point)
The ribbon file and surfaces do update *very slightly* but it’s largely ignoring our (sometimes large) edits. This pipeline worked well for us in version 6- do you have any idea what might be going on?
Would love to hear your thoughts about this.
Many thanks!!
Edan, Braindevlab@Princeton
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No, not really. If you get the data to me, I'll take a look if I can. Make sure to send specific information about vertices that you are having problems with so I don't have to go looking for it.
On 2/21/2022 6:29 PM, Edan Daniel wrote:
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Hi Doug, It is something we do *a lot* of, thus we hoped we'd be able to find a way to make the recon-wm implement our edits without additional manual edits, like we used to do with v6. Do you have any idea what could have caused this change in stubbornness in v7, or how would it be best to try to overcome this? We can try using the samseg stream as Bruce has kindly suggested, but we hoped to find a way to make our standard fs pipeline work with v7.
Many thanks!!! Edan @ PrincetonBrainDevLab
On Mon, Feb 21, 2022 at 5:04 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
If this is not something you have to do a lot of, you can put a repositioning point. See the release notes. On 2/21/2022 1:10 PM, Fischl, Bruce wrote:Hi Edan Control points might be helpful in both cases, but you are right it is more often the case when the wm is too dark. Another thing you can try is using expert options for mri_segment to constrain the intensity ranges of wm/gm. Or you could try using the samseg stream (someone else will have to help you with this, but it might well do better for your acquisitions) Cheers Bruce *From:* Edan Daniel <edand@princeton.edu> <mailto:edand@princeton.edu> *Sent:* Monday, February 21, 2022 11:14 AM *To:* Fischl, Bruce <BFISCHL@mgh.harvard.edu> <mailto:BFISCHL@mgh.harvard.edu> *Cc:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject:* Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0) * External Email - Use Caution * Thanks Bruce! This looks like a helpful solution for the places where the wm is not identified- we will definitely try it! We have one other type of issue which is more prevalent, that I was not sure if control points will be able to help with (we have not worked with control points before so sorry if this is a misinformed question) The main issue we're facing is that the final segmentation we get is too aggressive, that is, in many places too *many* voxels are categorized as wm and thus we have lower ability to characterize properties of the gray matter in the occipital cortex. What we usually do is clean the wm segmentation to make it less bulky, but now these edits are not being incorporated in the final segmentation. We are very confused by this because this type of edits were easily incorporated in v6, but not with v7. From my understanding- the control points would be helpful in the opposite case- where not enough voxels are recognized as wm (such as in the rightmost part of the attached image)- but not much in the rest of the image where we can see that the magenta borders (x.orig.nofix) are 'tighter' around the wm when compared to the borders after running through recon -wm (teal, x.white.preaparc). Is there a way to leverage the control points for this cause, or is there something else we can try to make the recon -wm less stubborn and accept our manual edits? For reference, the full command we run is as follows: recon-all -autorecon2-wm -autorecon3 -subjid ' freesurferfoldername ' -cc-crs ' num2str(corpus_point) Attaching another image - please let me know if the visibility here is better or if you'd like to see a different visualization. Many thanks!!!! Edan @ PrincetonBrainDevLab On Fri, Feb 18, 2022 at 9:53 AM Fischl, Bruce <BFISCHL@mgh.harvard.edu> wrote: Hi Edan It’s hard for me to see what’s going on in those images. What is the intensity of the white matter in the middle of the occipital strands in the brain.mgz and the brain.finalsurfs.mgz? If it is significantly lower than 110 you probably want some control points in the occipital lobe. Cheers Bruce *From:* Edan Daniel <edand@princeton.edu> *Sent:* Friday, February 18, 2022 12:15 AM *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; Fischl, Bruce <BFISCHL@mgh.harvard.edu> *Subject:* Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0) * External Email - Use Caution * Hi Bruce! We are focusing on the occipital lobe where the white matter boundary is often too far into the gray matter, and we need those voxels to record visual signals. Attaching a few images for reference - notice how much 'thicker' the wm segmentation is in the white.preaparc vs the lh.orig.nofix. wm edits of this sort were accepted when we were using the same pipeline with v6 (separate datasets), but now with v7 our edits get 're-corrected' and overwritten. We'd be happy to provide more information or images. Many thanks!!! Edan @ PrincetonBrainDevLab On Thu, Feb 17, 2022 at 7:01 PM Fischl, Bruce <BFISCHL@mgh.harvard.edu> wrote: Hi Edan Sometimes control points can be more effective than editing the wm, particularly if the intensities in that region are not what we expect (like if the wm and gm are darker than what we try to set them to). Can you post an image or two? Cheers Bruce *From:* freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Edan Daniel *Sent:* Thursday, February 17, 2022 6:51 PM *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> *Subject:* Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0) * External Email - Use Caution * * Different data, same pipeline. In v6 our changes were included in the final white surface segmentation, whereas in v7 they are overwritten during the placement 'refining'. * ?h.orig.nofix and ?h.orig DO reflect edits (?h.orig to some extent). white.preaparc does NOT. * We noticed that the placement is very stubborn and we were not able to overcome this. Methods like manually editing the wm surface worked well with v6 and do not work now with v7. We have also tried editing the filled.mgz with v7.2 following the new tutorial, and that did not work either. Is there any way we can overcome this stubbornness? Many thanks! Edan @ Princeton BrainDevLab On Thu, Feb 17, 2022 at 6:07 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote: The edits you are making only change the initial surface; the surface placement then refines the placement. Sometimes the surface placement can be quite stubborn. If this is the case, the ?h.orig.nofix and ?h.orig will reflect your edits (nofix exactly; ?h.orig to some extent). Also check the the white.preaparc is where the problem starts. When you say that v6 did better, do you mean on this same data or on different data? The surface placement has not changed that much since v6. On 2/14/2022 12:50 PM, Edan Daniel wrote: * External Email - Use Caution * We have been having issues with recreating the final surfaces after editing the white matter segmentation, which used to work smoothly in version 6. After running a subject through recon-all (version 7.1.1 *without* the parallel flag) and then editing the white matter, we run the following command (w v7.1.1): recon-all -autorecon2-wm -autorecon3 -subjid ' freesurferfoldername ' -cc-crs ' num2str(corpus_point) The ribbon file and surfaces do update *very slightly* but it’s largely ignoring our (sometimes large) edits. This pipeline worked well for us in version 6- do you have any idea what might be going on? Would love to hear your thoughts about this. Many thanks!! 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Douglas N. Greve -
Edan Daniel -
Fischl, Bruce