Hi everyone,
To put things into context, I am trying to follow the four step methodology outlined in this paper (Cohen-Adad, 2013) http://www.sciencedirect.com/science/article/pii/S1053811913000700
I have already performed recon-all on MPRAGE data. I have also carried out the following steps:
1) Reconstruct cortical surface 2) Register T1 to the surface 3) Sample T1 at a given cortical depth 4) Register surface to fsaverage
I have now been told to use the T2* information from the fourth echo of separately acquired T2* weighted data and to 'overlay' (I'm not sure if this is the correct usage of this technical term) it on the surfaces produced (as above) of the MPRAGE data. I realize that I can't perform recon-all on this T2* weighted data. I am assuming that I need to carry out steps similar to 1)-4) on this new data, but I'm not sure. Would you have any guidance on how to go about this?
Any help would be appreciated!
Thank you!
you can use bbregister to register your T2* volumes to the surface, then mri_vol2surf to sample and display it.
cheers Bruce On Tue, 23 Jul 2013, Smian wrote:
Hi everyone,
To put things into context, I am trying to follow the four step methodology outlined in this paper (Cohen-Adad, 2013) http://www.sciencedirect.com/science/article/pii/S1053811913000700
I have already performed recon-all on MPRAGE data. I have also carried out the following steps:
- Reconstruct cortical surface
- Register T1 to the surface
- Sample T1 at a given cortical depth
- Register surface to fsaverage
I have now been told to use the T2* information from the fourth echo of separately acquired T2* weighted data and to 'overlay' (I'm not sure if this is the correct usage of this technical term) it on the surfaces produced (as above) of the MPRAGE data. I realize that I can't perform recon-all on this T2* weighted data. I am assuming that I need to carry out steps similar to 1)-4) on this new data, but I'm not sure. Would you have any guidance on how to go about this?
Any help would be appreciated!
Thank you!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you for your reponse. The registration has turned out quite strangely (please see attached). I checked the first value in the mincost file and it is quite high (~0.95). I'm assuming that means that the initialization was bad. I tried changing the initialization from fsl to spm and header, but that failed too. Would you know why this could be occurring and how I might be able to fix it?
Thank you!
On 2013-07-23 16:07, Bruce Fischl wrote:
you can use bbregister to register your T2* volumes to the surface, then mri_vol2surf to sample and display it.
cheers Bruce On Tue, 23 Jul 2013, Smian wrote:
Hi everyone,
To put things into context, I am trying to follow the four step methodology outlined in this paper (Cohen-Adad, 2013) http://www.sciencedirect.com/science/article/pii/S1053811913000700
I have already performed recon-all on MPRAGE data. I have also carried out the following steps:
- Reconstruct cortical surface
- Register T1 to the surface
- Sample T1 at a given cortical depth
- Register surface to fsaverage
I have now been told to use the T2* information from the fourth echo of separately acquired T2* weighted data and to 'overlay' (I'm not sure if this is the correct usage of this technical term) it on the surfaces produced (as above) of the MPRAGE data. I realize that I can't perform recon-all on this T2* weighted data. I am assuming that I need to carry out steps similar to 1)-4) on this new data, but I'm not sure. Would you have any guidance on how to go about this?
Any help would be appreciated!
Thank you!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/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.
you need to give us your full command line otherwise it's impossible to figure out what went wrong. Also, is your data not whole brain? Can you describe it in more detal? On Tue, 23 Jul 2013, Smian wrote:
Thank you for your reponse. The registration has turned out quite strangely (please see attached). I checked the first value in the mincost file and it is quite high (~0.95). I'm assuming that means that the initialization was bad. I tried changing the initialization from fsl to spm and header, but that failed too. Would you know why this could be occurring and how I might be able to fix it?
Thank you!
On 2013-07-23 16:07, Bruce Fischl wrote:
you can use bbregister to register your T2* volumes to the surface, then mri_vol2surf to sample and display it.
cheers Bruce On Tue, 23 Jul 2013, Smian wrote:
Hi everyone,
To put things into context, I am trying to follow the four step methodology outlined in this paper (Cohen-Adad, 2013) http://www.sciencedirect.com/science/article/pii/S1053811913000700
I have already performed recon-all on MPRAGE data. I have also carried out the following steps:
- Reconstruct cortical surface
- Register T1 to the surface
- Sample T1 at a given cortical depth
- Register surface to fsaverage
I have now been told to use the T2* information from the fourth echo of separately acquired T2* weighted data and to 'overlay' (I'm not sure if this is the correct usage of this technical term) it on the surfaces produced (as above) of the MPRAGE data. I realize that I can't perform recon-all on this T2* weighted data. I am assuming that I need to carry out steps similar to 1)-4) on this new data, but I'm not sure. Would you have any guidance on how to go about this?
Any help would be appreciated!
Thank you!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/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.
What is your command line? This is surely an initialization error. Try running tkregister2 with --regheader to see where it starts. If that is close, then use --init-header on bbregister
doug
On 7/23/13 4:13 PM, Smian wrote:
Thank you for your reponse. The registration has turned out quite strangely (please see attached). I checked the first value in the mincost file and it is quite high (~0.95). I'm assuming that means that the initialization was bad. I tried changing the initialization from fsl to spm and header, but that failed too. Would you know why this could be occurring and how I might be able to fix it?
Thank you!
On 2013-07-23 16:07, Bruce Fischl wrote:
you can use bbregister to register your T2* volumes to the surface, then mri_vol2surf to sample and display it.
cheers Bruce On Tue, 23 Jul 2013, Smian wrote:
Hi everyone,
To put things into context, I am trying to follow the four step methodology outlined in this paper (Cohen-Adad, 2013) http://www.sciencedirect.com/science/article/pii/S1053811913000700
I have already performed recon-all on MPRAGE data. I have also carried out the following steps:
- Reconstruct cortical surface
- Register T1 to the surface
- Sample T1 at a given cortical depth
- Register surface to fsaverage
I have now been told to use the T2* information from the fourth echo of separately acquired T2* weighted data and to 'overlay' (I'm not sure if this is the correct usage of this technical term) it on the surfaces produced (as above) of the MPRAGE data. I realize that I can't perform recon-all on this T2* weighted data. I am assuming that I need to carry out steps similar to 1)-4) on this new data, but I'm not sure. Would you have any guidance on how to go about this?
Any help would be appreciated!
Thank you!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/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
Thank you for your response. I am pasting the command lines below, and attaching the images that correspond to each command line after tkregister2 is run.
command line for registration using all echos:
bbregister --s T1subject2 --mov [path]/T2star.nii.gz --reg [path]/registerT2allechos.dat --init-fsl --t2 --o [path]/T2starallechos_registeredtocorticalsurfacesubject2.nii
command line for registration using fourth echo only (as instructed):
bbregister --s T1subject2 --mov [path]/T2starecho4.nii.gz --reg [path]/registerT2starecho4.dat --init-reg [path]/registerT2allechos.dat --t2 --o [path]/T2starecho4_registeredtocorticalsurfacesubject2.nii
On 2013-07-23 23:45, Douglas Greve wrote:
What is your command line? This is surely an initialization error. Try running tkregister2 with --regheader to see where it starts. If that is close, then use --init-header on bbregister
doug
On 7/23/13 4:13 PM, Smian wrote:
Thank you for your reponse. The registration has turned out quite strangely (please see attached). I checked the first value in the mincost file and it is quite high (~0.95). I'm assuming that means that the initialization was bad. I tried changing the initialization from fsl to spm and header, but that failed too. Would you know why this could be occurring and how I might be able to fix it?
Thank you!
On 2013-07-23 16:07, Bruce Fischl wrote: you can use bbregister to register your T2* volumes to the surface, then mri_vol2surf to sample and display it.
cheers Bruce On Tue, 23 Jul 2013, Smian wrote:
Hi everyone,
To put things into context, I am trying to follow the four step methodology outlined in this paper (Cohen-Adad, 2013) http://www.sciencedirect.com/science/article/pii/S1053811913000700 [1]
I have already performed recon-all on MPRAGE data. I have also carried out the following steps:
- Reconstruct cortical surface
- Register T1 to the surface
- Sample T1 at a given cortical depth
- Register surface to fsaverage
I have now been told to use the T2* information from the fourth echo of separately acquired T2* weighted data and to 'overlay' (I'm not sure if this is the correct usage of this technical term) it on the surfaces produced (as above) of the MPRAGE data. I realize that I can't perform recon-all on this T2* weighted data. I am assuming that I need to carry out steps similar to 1)-4) on this new data, but I'm not sure. Would you have any guidance on how to go about this?
Any help would be appreciated!
Thank you!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer [2]
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer [2]
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 [3] . 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 [2]
Links:
[1] http://www.sciencedirect.com/science/article/pii/S1053811913000700 [2] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer [3] http://www.partners.org/complianceline
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.
Was T2star.nii.gz collected, or derived from something, collected in the same acquisition as the T1 analyzed by FS? If so, try using --init-header instead of --init-fsl. With a partial brain slab, FSL will surely fail. doug
On 07/24/2013 12:13 PM, Smian wrote:
Thank you for your response. I am pasting the command lines below, and attaching the images that correspond to each command line after tkregister2 is run.
command line for registration using all echos:
bbregister --s T1subject2 --mov [path]/T2star.nii.gz --reg [path]/registerT2allechos.dat --init-fsl --t2 --o [path]/T2starallechos_registeredtocorticalsurfacesubject2.nii
command line for registration using fourth echo only (as instructed):
bbregister --s T1subject2 --mov [path]/T2starecho4.nii.gz --reg [path]/registerT2starecho4.dat --init-reg [path]/registerT2allechos.dat --t2 --o [path]/T2starecho4_registeredtocorticalsurfacesubject2.nii
On 2013-07-23 23:45, Douglas Greve wrote:
What is your command line? This is surely an initialization error. Try running tkregister2 with --regheader to see where it starts. If that is close, then use --init-header on bbregister
doug
On 7/23/13 4:13 PM, Smian wrote:
Thank you for your reponse. The registration has turned out quite strangely (please see attached). I checked the first value in the mincost file and it is quite high (~0.95). I'm assuming that means that the initialization was bad. I tried changing the initialization from fsl to spm and header, but that failed too. Would you know why this could be occurring and how I might be able to fix it?
Thank you!
On 2013-07-23 16:07, Bruce Fischl wrote: you can use bbregister to register your T2* volumes to the surface, then mri_vol2surf to sample and display it.
cheers Bruce On Tue, 23 Jul 2013, Smian wrote:
Hi everyone,
To put things into context, I am trying to follow the four step methodology outlined in this paper (Cohen-Adad, 2013) http://www.sciencedirect.com/science/article/pii/S1053811913000700 [1]
I have already performed recon-all on MPRAGE data. I have also carried out the following steps:
- Reconstruct cortical surface
- Register T1 to the surface
- Sample T1 at a given cortical depth
- Register surface to fsaverage
I have now been told to use the T2* information from the fourth echo of separately acquired T2* weighted data and to 'overlay' (I'm not sure if this is the correct usage of this technical term) it on the surfaces produced (as above) of the MPRAGE data. I realize that I can't perform recon-all on this T2* weighted data. I am assuming that I need to carry out steps similar to 1)-4) on this new data, but I'm not sure. Would you have any guidance on how to go about this?
Any help would be appreciated!
Thank you!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer [2]
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer [2]
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 [3] . 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 [2]
Links:
[1] http://www.sciencedirect.com/science/article/pii/S1053811913000700 [2] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer [3] http://www.partners.org/complianceline
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
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Bruce Fischl -
Douglas Greve -
Douglas N Greve
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Smian