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 <ed...@princeton.edu>
<mailto:ed...@princeton.edu>
*Sent:* Monday, February 21, 2022 11:14 AM
*To:* Fischl, Bruce <bfis...@mgh.harvard.edu>
<mailto:bfis...@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
<bfis...@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 <ed...@princeton.edu>
*Sent:* Friday, February 18, 2022 12:15 AM
*To:* Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>; Fischl, Bruce
<bfis...@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
<bfis...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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
<dgr...@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>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://secure-web.cisco.com/1DjxybLd--ZLzgaQdLo2D5M19gv7Iqs7dtQ9T1jFojMmxBLD_jgyp_uRn2PLAev17NLMRF2LntFbMwZgMNN4j-5JvwKirqGFk7zMl3xSYVatI9gEvv90xHfWqglmQbbbYPnZysq79EXY_44U8CumuQEVStGDGbJrWFucGs-2p5t0b0G3tYCBsMLGnzSql6W34Dqaap2IISHt7eVki1PSwC5ehWJCnL-ZT_wLOW9fwda-uOi2jQtNcimUPdOGmmARulU1T2rfrBnQwQYscsWMAzJ-BtGyfZPwj-PWmk5UfZ40rWWL9Z1BPYQaCE_bshBt6/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
