[Freesurfer] Problems with manual grey matter editing

[Zamroziewicz, Marta Karolina]

Hello,

We have some reconstructions with a significant amount of grey matter excluded 
in the temporal cortex and are having problems using manual voxel editing to 
fix this.
Our correction process for brain tissue that wasn’t included in the pial/white 
matter outlines has been as follows:
1. When white matter is excluded from the white matter outline, we’ve used 
control points to identify missed white matter. We then re-run using the 
following command: recon-all -autorecon2-cp -autorecon3 -subjid .
2. When grey matter is excluded from the pial outline, we first make sure that 
white matter is outlined appropriately. If adding control points doesn’t fix 
the grey matter problem, we manually add grey matter voxels to the brainmask 
volume using the voxel edit tool. We then re-run using the following command: 
recon-all -autorecon-pial -subjid . In some cases (especially in the 
temporal cortex), the new reconstructions don’t incorporate the manually added 
grey matter voxels into the pial outline.
I’ve attached an image of a subject who didn’t have white matter problems but 
did have excluded grey matter in the temporal cortex. We reran this subject 
using the recon-all -autorecon-pial -subjid  command and the newly 
added grey matter voxels weren’t included in the new pial outline.

Is there a way to address this problem?

Thank you very much for your time!

Marta

_
Marta Zamroziewicz
MD/PhD Candidate
Decision Neuroscience Laboratory
University of Illinois Urbana-Champaign
mzam...@illinois.edu
815-980-3882
_

[cid:5F7AEAD8-4EA8-49CB-A4C2-7502236F5F01@beckman.uiuc.edu]
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[Freesurfer] BBRegister Patch

[Zamroziewicz, Marta Karolina]

Good morning!

Is the bbregister patch available yet (original email below)?

Thank you for your time and assistance!


Marta Zamroziewicz
MD/PhD Candidate
Decision Neuroscience Laboratory
University of Illinois Urbana-Champaign
mzam...@illinois.edu
815-980-3882





This email is related to the archived “bbregister and FLAIR” email chain posted 
by Kayle Sawyer on 5/23/2014 
(http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg36117.html).

We have also been registering with FLAIR scans, and have run into a problem 
with approximately half of our subjects. Recon-all completes successfully but a 
bad registration step leaves our MPRAGE and FLAIR scans misaligned. I’ve 
attached two screenshots, the first of which shows a bad registration and the 
second of which shows a good registration.

Per your previous suggestion, we ran bbregister using the following flag:

bbregister --s SLOTS007 --mov flair.mgz --init-header --reg reg.test.dat
--t2 --lta reg.test.lta

This did result in a good registration, and we are hoping to incorporate this 
into our processing pipeline to ensure that we can use the FLAIR for refining 
the pill surface. The problem that we’ve run into is that we aren’t sure at 
which point this bbregister step occurs within the recon-all process flow. We 
were thinking there are a couple of possibilities:

1. manually create the transformation matrix for the FLAIR using the command 
mentioned above, and then re-run whichever steps necessary in recon-all to 
include this manually created xform;

2. apply the manually created xform to the mri/orig/FLAIRraw.mgz image to 
create a new, properly aligned mri/FLAIR.mgz, and then re-run recon-all with 
whatever steps/flags we need to include this FLAIR image to refine the pial 
surface.

Unfortunately we're not exactly sure which flags to include in recon-all in 
order to most efficiently re-process our data with the manually created FLAIR 
transformation, and we were hoping you might offer some advice on this point. 
Please let me know if I can provide any additional information.




[cid:32781EBE-87CB-4FF9-815F-4D732E675168@beckman.uiuc.edu][cid:45A8FE84-7BD3-4C2E-8618-AE9786828CF2@beckman.uiuc.edu]


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[Freesurfer] Checking in about FLAIR Registration Problem

[Zamroziewicz, Marta Karolina]

Good morning,

I wrote several weeks ago about a bbregister problem that we’ve encountered 
(I’ve attached the original email below). I’d like to check back in about the 
status of the patch that was being developed.

Thank you for your time and assistance!

Marta Zamroziewicz
MD/PhD Candidate
Decision Neuroscience Laboratory
University of Illinois Urbana-Champaign
mzam...@illinois.edu
815-980-3882

This email is related to the archived “bbregister and FLAIR” email chain posted 
by Kayle Sawyer on 5/23/2014 
(http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg36117.html).

We have also been registering with FLAIR scans, and have run into a problem 
with approximately half of our subjects. Recon-all completes successfully but a 
bad registration step leaves our MPRAGE and FLAIR scans misaligned. I’ve 
attached two screenshots, the first of which shows a bad registration and the 
second of which shows a good registration.

Per your previous suggestion, we ran bbregister using the following flag:

bbregister --s SLOTS007 --mov flair.mgz --init-header --reg reg.test.dat
--t2 --lta reg.test.lta

This did result in a good registration, and we are hoping to incorporate this 
into our processing pipeline to ensure that we can use the FLAIR for refining 
the pill surface. The problem that we’ve run into is that we aren’t sure at 
which point this bbregister step occurs within the recon-all process flow. We 
were thinking there are a couple of possibilities:

1. manually create the transformation matrix for the FLAIR using the command 
mentioned above, and then re-run whichever steps necessary in recon-all to 
include this manually created xform;

2. apply the manually created xform to the mri/orig/FLAIRraw.mgz image to 
create a new, properly aligned mri/FLAIR.mgz, and then re-run recon-all with 
whatever steps/flags we need to include this FLAIR image to refine the pial 
surface.

Unfortunately we're not exactly sure which flags to include in recon-all in 
order to most efficiently re-process our data with the manually created FLAIR 
transformation, and we were hoping you might offer some advice on this point. 
Please let me know if I can provide any additional information.




[cid:795E512B-0727-4B3D-8B43-17BE1640FBD8@beckman.uiuc.edu][cid:9003C1C6-AA59-46E3-BF4A-0CEE22C57030@beckman.uiuc.edu]







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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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dispose of the e-mail.

Re: [Freesurfer] Checking Back In: FLAIR Registration Problems

[Zamroziewicz, Marta Karolina]

Good afternoon,

I'm just checking in about a bbregister problem I emailed about last week (see 
email chain below).

Thank you very much!

Marta Zamroziewicz
MD/PhD Candidate
Decision Neuroscience Laboratory
University of Illinois Urbana-Champaign
mzam...@illinois.edu<mailto:mzam...@illinois.edu>
815-980-3882

On Aug 1, 2014, at 9:19 AM, "Zamroziewicz, Marta Karolina" 
mailto:mzam...@illinois.edu>> wrote:

Good morning,

I’m just checking back in about a bbregister problem that I posted about 
earlier this week (see email below). I was told to check back at the end of the 
week about a patch.

Thanks so much for your time and assistance!

Marta Zamroziewicz
MD/PhD Candidate
Decision Neuroscience Laboratory
University of Illinois Urbana-Champaign
mzam...@illinois.edu<mailto:mzam...@illinois.edu>


Begin forwarded message:

From: "Zamroziewicz, Marta Karolina" 
mailto:mzam...@illinois.edu>>
Subject: [Freesurfer] FLAIR Registration Problems
Date: July 29, 2014 at 1:57:58 PM CDT
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>

Hello,

This email is related to the archived “bbregister and FLAIR” email chain posted 
by Kayle Sawyer on 5/23/2014 
(http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg36117.html).

We have also been registering with FLAIR scans, and have run into a problem 
with approximately half of our subjects. Recon-all completes successfully but a 
bad registration step leaves our MPRAGE and FLAIR scans misaligned. I’ve 
attached two screenshots, the first of which shows a bad registration and the 
second of which shows a good registration.

Per your previous suggestion, we ran bbregister using the following flag:

bbregister --s SLOTS007 --mov flair.mgz --init-header --reg reg.test.dat
--t2 --lta reg.test.lta

This did result in a good registration, and we are hoping to incorporate this 
into our processing pipeline to ensure that we can use the FLAIR for refining 
the pill surface. The problem that we’ve run into is that we aren’t sure at 
which point this bbregister step occurs within the recon-all process flow. We 
were thinking there are a couple of possibilities:

1. manually create the transformation matrix for the FLAIR using the command 
mentioned above, and then re-run whichever steps necessary in recon-all to 
include this manually created xform;

2. apply the manually created xform to the mri/orig/FLAIRraw.mgz image to 
create a new, properly aligned mri/FLAIR.mgz, and then re-run recon-all with 
whatever steps/flags we need to include this FLAIR image to refine the pial 
surface.

Unfortunately we're not exactly sure which flags to include in recon-all in 
order to most efficiently re-process our data with the manually created FLAIR 
transformation, and we were hoping you might offer some advice on this point. 
Please let me know if I can provide any additional information.

Thanks for your time and assistance!








Marta Zamroziewicz
MD/PhD Candidate
Decision Neuroscience Laboratory
University of Illinois Urbana-Champaign
mzam...@illinois.edu<mailto:mzam...@illinois.edu>


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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Checking Back In: FLAIR Registration Problems

[Zamroziewicz, Marta Karolina]

Good morning,

I’m just checking back in about a bbregister problem that I posted about 
earlier this week (see email below). I was told to check back at the end of the 
week about a patch.

Thanks so much for your time and assistance!

Marta Zamroziewicz
MD/PhD Candidate
Decision Neuroscience Laboratory
University of Illinois Urbana-Champaign
mzam...@illinois.edu<mailto:mzam...@illinois.edu>


Begin forwarded message:

From: "Zamroziewicz, Marta Karolina" 
mailto:mzam...@illinois.edu>>
Subject: [Freesurfer] FLAIR Registration Problems
Date: July 29, 2014 at 1:57:58 PM CDT
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>

Hello,

This email is related to the archived “bbregister and FLAIR” email chain posted 
by Kayle Sawyer on 5/23/2014 
(http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg36117.html).

We have also been registering with FLAIR scans, and have run into a problem 
with approximately half of our subjects. Recon-all completes successfully but a 
bad registration step leaves our MPRAGE and FLAIR scans misaligned. I’ve 
attached two screenshots, the first of which shows a bad registration and the 
second of which shows a good registration.

Per your previous suggestion, we ran bbregister using the following flag:

bbregister --s SLOTS007 --mov flair.mgz --init-header --reg reg.test.dat
--t2 --lta reg.test.lta

This did result in a good registration, and we are hoping to incorporate this 
into our processing pipeline to ensure that we can use the FLAIR for refining 
the pill surface. The problem that we’ve run into is that we aren’t sure at 
which point this bbregister step occurs within the recon-all process flow. We 
were thinking there are a couple of possibilities:

1. manually create the transformation matrix for the FLAIR using the command 
mentioned above, and then re-run whichever steps necessary in recon-all to 
include this manually created xform;

2. apply the manually created xform to the mri/orig/FLAIRraw.mgz image to 
create a new, properly aligned mri/FLAIR.mgz, and then re-run recon-all with 
whatever steps/flags we need to include this FLAIR image to refine the pial 
surface.

Unfortunately we're not exactly sure which flags to include in recon-all in 
order to most efficiently re-process our data with the manually created FLAIR 
transformation, and we were hoping you might offer some advice on this point. 
Please let me know if I can provide any additional information.

Thanks for your time and assistance!



[cid:D837E275-197C-46BB-A1D4-B7559DF58D48@beckman.uiuc.edu][cid:D62F65DB-AF9A-4ADC-A596-79E0821DE24D@beckman.uiuc.edu]




Marta Zamroziewicz
MD/PhD Candidate
Decision Neuroscience Laboratory
University of Illinois Urbana-Champaign
mzam...@illinois.edu<mailto:mzam...@illinois.edu>


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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] FLAIR Registration Problems

[Zamroziewicz, Marta Karolina]

Hello,

This email is related to the archived “bbregister and FLAIR” email chain posted 
by Kayle Sawyer on 5/23/2014 
(http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg36117.html).

We have also been registering with FLAIR scans, and have run into a problem 
with approximately half of our subjects. Recon-all completes successfully but a 
bad registration step leaves our MPRAGE and FLAIR scans misaligned. I’ve 
attached two screenshots, the first of which shows a bad registration and the 
second of which shows a good registration.

Per your previous suggestion, we ran bbregister using the following flag:

bbregister --s SLOTS007 --mov flair.mgz --init-header --reg reg.test.dat
--t2 --lta reg.test.lta

This did result in a good registration, and we are hoping to incorporate this 
into our processing pipeline to ensure that we can use the FLAIR for refining 
the pill surface. The problem that we’ve run into is that we aren’t sure at 
which point this bbregister step occurs within the recon-all process flow. We 
were thinking there are a couple of possibilities:

1. manually create the transformation matrix for the FLAIR using the command 
mentioned above, and then re-run whichever steps necessary in recon-all to 
include this manually created xform;

2. apply the manually created xform to the mri/orig/FLAIRraw.mgz image to 
create a new, properly aligned mri/FLAIR.mgz, and then re-run recon-all with 
whatever steps/flags we need to include this FLAIR image to refine the pial 
surface.

Unfortunately we're not exactly sure which flags to include in recon-all in 
order to most efficiently re-process our data with the manually created FLAIR 
transformation, and we were hoping you might offer some advice on this point. 
Please let me know if I can provide any additional information.

Thanks for your time and assistance!



[cid:D837E275-197C-46BB-A1D4-B7559DF58D48@beckman.uiuc.edu][cid:D62F65DB-AF9A-4ADC-A596-79E0821DE24D@beckman.uiuc.edu]




Marta Zamroziewicz
MD/PhD Candidate
Decision Neuroscience Laboratory
University of Illinois Urbana-Champaign
mzam...@illinois.edu
815-980-3882

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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.