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 mzamro2@illinois.edumailto:mzamro2@illinois.edu 815-980-3882
The current version of recon-all does not have any flexibility with regard to bbr. I'm developing a patch that will allow this to be fixed. Check back at the end of the week. doug
On 07/29/2014 02:57 PM, Zamroziewicz, Marta Karolina wrote:
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:
- 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;
- 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 mzamro2@illinois.edu mailto:mzamro2@illinois.edu 815-980-3882
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 mzamro2@illinois.edumailto:mzamro2@illinois.edu
Begin forwarded message:
From: "Zamroziewicz, Marta Karolina" <mzamro2@illinois.edumailto:mzamro2@illinois.edu> Subject: [Freesurfer] FLAIR Registration Problems Date: July 29, 2014 at 1:57:58 PM CDT To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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 mzamro2@illinois.edumailto:mzamro2@illinois.edu
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Hi Marta, I thought I was going to be ready to release it today, but my checks failed on the new script, so now I have to dig into it to see what is wrong. Check back next week. doug
On 08/01/2014 09:19 AM, Zamroziewicz, Marta Karolina 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 mzamro2@illinois.edu mailto:mzamro2@illinois.edu
Begin forwarded message:
*From: *"Zamroziewicz, Marta Karolina" <mzamro2@illinois.edu mailto:mzamro2@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" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> *Reply-To: * Freesurfer support list <freesurfer@nmr.mgh.harvard.edu 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:
- 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;
- 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 mzamro2@illinois.edu mailto:mzamro2@illinois.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 mzamro2@illinois.edumailto:mzamro2@illinois.edu 815-980-3882
On Aug 1, 2014, at 9:19 AM, "Zamroziewicz, Marta Karolina" <mzamro2@illinois.edumailto:mzamro2@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 mzamro2@illinois.edumailto:mzamro2@illinois.edu
Begin forwarded message:
From: "Zamroziewicz, Marta Karolina" <mzamro2@illinois.edumailto:mzamro2@illinois.edu> Subject: [Freesurfer] FLAIR Registration Problems Date: July 29, 2014 at 1:57:58 PM CDT To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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!
<Screen Shot 2014-07-29 at 9.29.45 AM.jpeg><Screen Shot 2014-07-29 at 9.31.26 AM.jpeg>
Marta Zamroziewicz MD/PhD Candidate Decision Neuroscience Laboratory University of Illinois Urbana-Champaign mzamro2@illinois.edumailto:mzamro2@illinois.edu
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
I have put a new recon-all here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/recon-all
You can try adding -bbr-init-header to the recon-all command-line
This also fixes a bug in that the statistics were computed before the T2 was used to refine the pial surface.
doug
On 08/09/2014 12:13 PM, Zamroziewicz, Marta Karolina wrote:
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 mzamro2@illinois.edu mailto:mzamro2@illinois.edu 815-980-3882
On Aug 1, 2014, at 9:19 AM, "Zamroziewicz, Marta Karolina" <mzamro2@illinois.edu mailto:mzamro2@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 mzamro2@illinois.edu mailto:mzamro2@illinois.edu
Begin forwarded message:
*From: *"Zamroziewicz, Marta Karolina" <mzamro2@illinois.edu mailto:mzamro2@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" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> *Reply-To: * Freesurfer support list <freesurfer@nmr.mgh.harvard.edu 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:
- 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;
- 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!
<Screen Shot 2014-07-29 at 9.29.45 AM.jpeg><Screen Shot 2014-07-29 at 9.31.26 AM.jpeg>
Marta Zamroziewicz MD/PhD Candidate Decision Neuroscience Laboratory University of Illinois Urbana-Champaign mzamro2@illinois.edu mailto:mzamro2@illinois.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Zamroziewicz, Marta Karolina