[Freesurfer] problem bbregister onto longitudinal pipeline
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 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.
Re: [Freesurfer] problem bbregister onto longitudinal pipeline
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 > > ___ 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.
Re: [Freesurfer] problem bbregister onto longitudinal pipeline
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 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: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ 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.
Re: [Freesurfer] problem bbregister onto longitudinal pipeline
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 > 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: >mreu...@nmr.mgh.harvard.edu >reu...@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
Re: [Freesurfer] problem bbregister onto longitudinal pipeline
Which one failed? Bruce On Jun 20, 2013, at 10:29 AM, Daniel Garcia 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 >> 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: >> mreu...@nmr.mgh.harvard.edu >> reu...@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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] problem bbregister onto longitudinal pipeline
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 > 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 > >> 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: > >> mreu...@nmr.mgh.harvard.edu > >> reu...@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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] problem bbregister onto longitudinal pipeline
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 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 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: mreu...@nmr.mgh.harvard.edu reu...@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 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.
