Re: [Freesurfer] problem with pial surface reconstruction using T1 (MPRAGE) and T2 (SPACE) weighted images
Dear Bruce & Matt,
thank you for your help.
@Bruce: I would be happy to send you the data, just let me know by e-mail which files you would need.
@Matt: Could you please specify the commands for the flags -nsigma_above and -nsigma_below and how you would rerun the pipeline? Also what values would be recommended?
I did not find any manual/help files regarding the flags, so it would be helpful to document it.
NB. I found another thread in the maillist which probably relates to the issue: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033550... . However I could not verify this, due to expired dropbox files.
Yours,
Emil
Probably Emil¹s current example would be best because it is failing in your recon-all setup.
Matt.
On 5/9/14, 9:31 AM, "Bruce Fischl" fis...@nmr.mgh.harvard.edu wrote:
Hi Matt
if you can send me an example I'll try to find time to take a look Bruce On Fri, 9 May 2014, Matt Glasser wrote:
Hi Bruce,
For whatever reason, sometimes the T2w surface adjustment will be way off. Adjusting the -nsigma_above <#> -nsigma_below <#> even a little bit up and down can get it out of the minimum and make it work, so there might be a bug.
Peace,
Matt.
From: "Emil H.J. Nijhuis" emil.nijh...@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, May 9, 2014 at 4:53 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] problem with pial surface reconstruction using T1 (MPRAGE) and T2 (SPACE) weighted images
Dear Bruce,
thank you for your help.
attached I have put an fslview, tkmedit screen-shot of the T2 image and a tk surfer image of lh.woT2.pial.
It appears that without consideration of the T2 this effect does not happen.
What would be your recommendation if I would like to keep using the T2 weigh ted image?
Yours, Emil
Hi Emil
how do the surfaces look before you apply the T2 deformation? And how do they look visualized over the T2 instead of the T1?
cheers Bruce
On Thu, 8 May 2014, Emil H.J. Nijhuis wrote:
Hi,
I have been using Freesurfer v5.3 to perform surface reconstruct for 1mm isotropic T1 (MPRAGE) and T2 (SPACE) weighted images from a Siemens 3T Trio scanner with a 32-channel head coil. Unfortunately for half of my subjects I receive an rather odd pial surface artefact, while the 'white' surfaces do not suffer from the same issue.
The command line I have used was:
recon-all -all -subjid <subjectid> -T2 <subjectdir>/mri/orig/T2.mgz -T2pial -3T
Are you familiar with this issue and do you have some advice for me?
Thank you very much for your help.
Yours sincerely,
Emil
--
Emil H.J. Nijhuis, PhD Researcher - Division of Diagnostic and Interventional Neuroradiology University Hospital Basel Petersgraben 4 CH 4031 Basel Switzerland
Freesurfer mailing list
freesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/li sti nfo/freesurfer _______________________________________________ Freesurfer mailing list 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
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 Emil
I would need the entire subject dir plus the T2-space volume
cheers Bruce On Tue, 13 May 2014, Emil H.J. Nijhuis wrote:
Dear Bruce & Matt, thank you for your help.
@Bruce: I would be happy to send you the data, just let me know by e-mail which files you wo uld need.
@Matt: Could you please specify the commands for the flags -nsigma_above and -nsigma_below a nd how you would rerun the pipeline? Also what values would be recommended?
I did not find any manual/help files regarding the flags, so it would be helpful to document it.
NB. I found another thread in the maillist which probably relates to the issue: https://mail .nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033550.html . However I could not verify this, due to expired dropbox files.
Yours,
Emil
Probably Emil¹s current example would be best because it is failing in your recon-all setup.
Matt.
On 5/9/14, 9:31 AM, "Bruce Fischl" fis...@nmr.mgh.harvard.edu wrote:
Hi Matt
if you can send me an example I'll try to find time to take a look Bruce On Fri, 9 May 2014, Matt Glasser wrote:
Hi Bruce,
For whatever reason, sometimes the T2w surface adjustment will be way off. Adjusting the -nsigma_above <#> -nsigma_below <#> even a little bit up and down can get it out of the minimum and make it work, so there might be a bug.
Peace,
Matt.
From: "Emil H.J. Nijhuis" emil.nijh...@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, May 9, 2014 at 4:53 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] problem with pial surface reconstruction using T1 (MPRAGE) and T2 (SPACE) weighted images
Dear Bruce,
thank you for your help.
attached I have put an fslview, tkmedit screen-shot of the T2 image and a tk surfer image of lh.woT2.pial.
It appears that without consideration of the T2 this effect does not happen.
What would be your recommendation if I would like to keep using the T2 weigh ted image?
Yours, Emil
Hi Emil
how do the surfaces look before you apply the T2 deformation? And how do they look visualized over the T2 instead of the T1?
cheers Bruce
On Thu, 8 May 2014, Emil H.J. Nijhuis wrote:
Hi,
I have been using Freesurfer v5.3 to perform surface reconstruct for 1mm isotropic T1 (MPRAGE) and T2 (SPACE) weighted images from a Siemens 3T Trio scanner with a 32-channel head coil. Unfortunately for half of my subjects I receive an rather odd pial surface artefact, while the 'white' surfaces do not suffer from the same issue.
The command line I have used was:
recon-all -all -subjid <subjectid> -T2 <subjectdir>/mri/orig/T2.mgz -T2pial -3T
Are you familiar with this issue and do you have some advice for me?
Thank you very much for your help.
Yours sincerely,
Emil
--
Emil H.J. Nijhuis, PhD Researcher - Division of Diagnostic and Interventional Neuroradiology University Hospital Basel Petersgraben 4 CH 4031 Basel Switzerland
Freesurfer mailing list
freesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/li sti nfo/freesurfer _______________________________________________ Freesurfer mailing list 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
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 don’t know if recon-all will pass those flags in or not. Probably best to let Bruce take a look.
Peace,
Matt.
On 5/13/14, 7:36 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Emil
I would need the entire subject dir plus the T2-space volume
cheers Bruce On Tue, 13 May 2014, Emil H.J. Nijhuis wrote:
Dear Bruce & Matt, thank you for your help.
@Bruce: I would be happy to send you the data, just let me know by e-mail which files you wo uld need.
@Matt: Could you please specify the commands for the flags -nsigma_above and -nsigma_below a nd how you would rerun the pipeline? Also what values would be recommended?
I did not find any manual/help files regarding the flags, so it would be helpful to document it.
NB. I found another thread in the maillist which probably relates to the issue: https://mail .nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033550.html . However I could not verify this, due to expired dropbox files.
Yours,
Emil
Probably Emil¹s current example would be best because it is failing in your recon-all setup.
Matt.
On 5/9/14, 9:31 AM, "Bruce Fischl" fis...@nmr.mgh.harvard.edu wrote:
Hi Matt
if you can send me an example I'll try to find time to take a look Bruce On Fri, 9 May 2014, Matt Glasser wrote:
Hi Bruce,
For whatever reason, sometimes the T2w surface adjustment will be way off. Adjusting the -nsigma_above <#> -nsigma_below <#> even a little bit
up
and down can get it out of the minimum and make it work, so there might
be a
bug.
Peace,
Matt.
From: "Emil H.J. Nijhuis" emil.nijh...@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, May 9, 2014 at 4:53 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] problem with pial surface reconstruction using T1 (MPRAGE) and T2 (SPACE) weighted images
Dear Bruce,
thank you for your help.
attached I have put an fslview, tkmedit screen-shot of the T2 image
and
a tk surfer image of lh.woT2.pial.
It appears that without consideration of the T2 this effect does not happen.
What would be your recommendation if I would like to keep using the
T2
weigh ted image?
Yours, Emil
Hi Emil
how do the surfaces look before you apply the T2 deformation? And
how do
they look visualized over the T2 instead of the T1?
cheers Bruce
On Thu, 8 May 2014, Emil H.J. Nijhuis wrote:
Hi,
I have been using Freesurfer v5.3 to perform surface reconstruct for
1mm
isotropic T1 (MPRAGE) and T2 (SPACE) weighted images from a Siemens
3T
Trio scanner with a 32-channel head coil. Unfortunately for half of my subjects I receive an rather odd pial surface artefact, while the 'white'
surfaces
do not suffer from the same issue.
The command line I have used was:
recon-all -all -subjid <subjectid> -T2 <subjectdir>/mri/orig/T2.mgz -T2pial -3T
Are you familiar with this issue and do you have some advice for me?
Thank you very much for your help.
Yours sincerely,
Emil
--
Emil H.J. Nijhuis, PhD Researcher - Division of Diagnostic and Interventional Neuroradiology University Hospital Basel Petersgraben 4 CH 4031 Basel Switzerland
Freesurfer mailing list
freesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/ li sti nfo/freesurfer _______________________________________________ Freesurfer mailing
list
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
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
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@nmr.mgh.harvard.edu
-
Bruce Fischl -
Emil H.J. Nijhuis -
Matt Glasser