Dear Freesurfer Users,
I'm having a problem to register my PET images into the longitudinal pipeline of freesurfer (version 5.1).
I have use bbregister without any problem to put the PET image into the crossectional images but it fails to register to the long version of it. Someone can tell me if I'm doing something wrong?
bbregister -s P09_TA --mov pet_09.nii --init-fsl --reg matrix.mat --o pet2free.mgz
This last command works perfectly, but
bbregister -s P09_TA.long.P09 --mov pet_09.nii --init-fsl --reg matrix.mat --o pet2free.mgz
Fails completely.
My objective is to project my pet cortex into the surface in longitudinal that is why I'm interested in this processing. Maybe you can tell my another way of doing this.
Thank you very much.
Daniel
Hi Daniel, "fails completely" is not very informative. Can you send the bbr log file? doug
On 6/14/13 3:25 AM, Daniel Garcia wrote:
Dear Freesurfer Users,
I'm having a problem to register my PET images into the longitudinal pipeline of freesurfer (version 5.1).
I have use bbregister without any problem to put the PET image into the crossectional images but it fails to register to the long version of it. Someone can tell me if I'm doing something wrong?
bbregister -s P09_TA --mov pet_09.nii --init-fsl --reg matrix.mat --o pet2free.mgz
This last command works perfectly, but
bbregister -s P09_TA.long.P09 --mov pet_09.nii --init-fsl --reg matrix.mat --o pet2free.mgz
Fails completely.
My objective is to project my pet cortex into the surface in longitudinal that is why I'm interested in this processing. Maybe you can tell my another way of doing this.
Thank you very much.
Daniel
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Daniel,
bbregister is completely independent of the longitudinal stream, so if it fails, it has other reasons (e.g. bad initial alignment). You could try to switch the initial alignment to some other methods.
Best, Martin
On Jun 14, 2013, at 3:25 AM, Daniel Garcia d.garcia-ihu@icm-institute.org wrote:
Dear Freesurfer Users,
I'm having a problem to register my PET images into the longitudinal pipeline of freesurfer (version 5.1).
I have use bbregister without any problem to put the PET image into the crossectional images but it fails to register to the long version of it. Someone can tell me if I'm doing something wrong?
bbregister -s P09_TA --mov pet_09.nii --init-fsl --reg matrix.mat --o pet2free.mgz
This last command works perfectly, but
bbregister -s P09_TA.long.P09 --mov pet_09.nii --init-fsl --reg matrix.mat --o pet2free.mgz
Fails completely.
My objective is to project my pet cortex into the surface in longitudinal that is why I'm interested in this processing. Maybe you can tell my another way of doing this.
Thank you very much.
Daniel
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--------------------------------- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129
Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu
Hello all,
Thank you very much for your comments and sorry for not being too precise with my problem before.
It seemed at the begining to me very strange that the same image processed in crossectional or longitudinal had different results in registration and I thought it was something related to that more than the initialization
I changed the initialization and it seems to work. Thank you very much.
Daniel
Le mercredi 19 juin 2013 à 20:32 -0400, Martin Reuter a écrit :
Hi Daniel,
bbregister is completely independent of the longitudinal stream, so if it fails, it has other reasons (e.g. bad initial alignment). You could try to switch the initial alignment to some other methods.
Best, Martin
On Jun 14, 2013, at 3:25 AM, Daniel Garcia d.garcia-ihu@icm-institute.org wrote:
Dear Freesurfer Users,
I'm having a problem to register my PET images into the longitudinal pipeline of freesurfer (version 5.1).
I have use bbregister without any problem to put the PET image into the crossectional images but it fails to register to the long version of it. Someone can tell me if I'm doing something wrong?
bbregister -s P09_TA --mov pet_09.nii --init-fsl --reg matrix.mat --o pet2free.mgz
This last command works perfectly, but
bbregister -s P09_TA.long.P09 --mov pet_09.nii --init-fsl --reg matrix.mat --o pet2free.mgz
Fails completely.
My objective is to project my pet cortex into the surface in longitudinal that is why I'm interested in this processing. Maybe you can tell my another way of doing this.
Thank you very much.
Daniel
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129
Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu
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.
Which one failed? Bruce
On Jun 20, 2013, at 10:29 AM, Daniel Garcia d.garcia-ihu@icm-institute.org wrote:
Hello all,
Thank you very much for your comments and sorry for not being too precise with my problem before.
It seemed at the begining to me very strange that the same image processed in crossectional or longitudinal had different results in registration and I thought it was something related to that more than the initialization
I changed the initialization and it seems to work. Thank you very much.
Daniel
Le mercredi 19 juin 2013 à 20:32 -0400, Martin Reuter a écrit :
Hi Daniel,
bbregister is completely independent of the longitudinal stream, so if it fails, it has other reasons (e.g. bad initial alignment). You could try to switch the initial alignment to some other methods.
Best, Martin
On Jun 14, 2013, at 3:25 AM, Daniel Garcia d.garcia-ihu@icm-institute.org wrote:
Dear Freesurfer Users,
I'm having a problem to register my PET images into the longitudinal pipeline of freesurfer (version 5.1).
I have use bbregister without any problem to put the PET image into the crossectional images but it fails to register to the long version of it. Someone can tell me if I'm doing something wrong?
bbregister -s P09_TA --mov pet_09.nii --init-fsl --reg matrix.mat --o pet2free.mgz
This last command works perfectly, but
bbregister -s P09_TA.long.P09 --mov pet_09.nii --init-fsl --reg matrix.mat --o pet2free.mgz
Fails completely.
My objective is to project my pet cortex into the surface in longitudinal that is why I'm interested in this processing. Maybe you can tell my another way of doing this.
Thank you very much.
Daniel
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129
Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu
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 longitudinal one, about 20 mm out of the good registration
Le jeudi 20 juin 2013 à 10:36 -0400, Bruce Fischl a écrit :
Which one failed? Bruce
On Jun 20, 2013, at 10:29 AM, Daniel Garcia d.garcia-ihu@icm-institute.org wrote:
Hello all,
Thank you very much for your comments and sorry for not being too precise with my problem before.
It seemed at the begining to me very strange that the same image processed in crossectional or longitudinal had different results in registration and I thought it was something related to that more than the initialization
I changed the initialization and it seems to work. Thank you very much.
Daniel
Le mercredi 19 juin 2013 à 20:32 -0400, Martin Reuter a écrit :
Hi Daniel,
bbregister is completely independent of the longitudinal stream, so if it fails, it has other reasons (e.g. bad initial alignment). You could try to switch the initial alignment to some other methods.
Best, Martin
On Jun 14, 2013, at 3:25 AM, Daniel Garcia d.garcia-ihu@icm-institute.org wrote:
Dear Freesurfer Users,
I'm having a problem to register my PET images into the longitudinal pipeline of freesurfer (version 5.1).
I have use bbregister without any problem to put the PET image into the crossectional images but it fails to register to the long version of it. Someone can tell me if I'm doing something wrong?
bbregister -s P09_TA --mov pet_09.nii --init-fsl --reg matrix.mat --o pet2free.mgz
This last command works perfectly, but
bbregister -s P09_TA.long.P09 --mov pet_09.nii --init-fsl --reg matrix.mat --o pet2free.mgz
Fails completely.
My objective is to project my pet cortex into the surface in longitudinal that is why I'm interested in this processing. Maybe you can tell my another way of doing this.
Thank you very much.
Daniel
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129
Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu
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
I meant which initialization - FSL or SPM? On Thu, 20 Jun 2013, Daniel Garcia wrote:
The longitudinal one, about 20 mm out of the good registration
Le jeudi 20 juin 2013 à 10:36 -0400, Bruce Fischl a écrit :
Which one failed? Bruce
On Jun 20, 2013, at 10:29 AM, Daniel Garcia d.garcia-ihu@icm-institute.org wrote:
Hello all,
Thank you very much for your comments and sorry for not being too precise with my problem before.
It seemed at the begining to me very strange that the same image processed in crossectional or longitudinal had different results in registration and I thought it was something related to that more than the initialization
I changed the initialization and it seems to work. Thank you very much.
Daniel
Le mercredi 19 juin 2013 à 20:32 -0400, Martin Reuter a écrit :
Hi Daniel,
bbregister is completely independent of the longitudinal stream, so if it fails, it has other reasons (e.g. bad initial alignment). You could try to switch the initial alignment to some other methods.
Best, Martin
On Jun 14, 2013, at 3:25 AM, Daniel Garcia d.garcia-ihu@icm-institute.org wrote:
Dear Freesurfer Users,
I'm having a problem to register my PET images into the longitudinal pipeline of freesurfer (version 5.1).
I have use bbregister without any problem to put the PET image into the crossectional images but it fails to register to the long version of it. Someone can tell me if I'm doing something wrong?
bbregister -s P09_TA --mov pet_09.nii --init-fsl --reg matrix.mat --o pet2free.mgz
This last command works perfectly, but
bbregister -s P09_TA.long.P09 --mov pet_09.nii --init-fsl --reg matrix.mat --o pet2free.mgz
Fails completely.
My objective is to project my pet cortex into the surface in longitudinal that is why I'm interested in this processing. Maybe you can tell my another way of doing this.
Thank you very much.
Daniel
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129
Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu
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
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Bruce Fischl -
Daniel Garcia -
Douglas Greve -
Martin Reuter