Dear Joana,
Two things:
1. You should be very careful to use fslswapdim since it may result in an unintended left-right flipping. It's better to use fslreorient2std.
2. The tool dt-recon computes the coregistration of the lowb volume to the anatomical volume, see register.dat. You can then use the following to coregister FA:
mri_vol2vol --reg register.dat --mov fa.nii --o fa-ana.nii -targ subject/mri/T1.mgz
where "subject" is the output folder generated by the recon-all command. You should not forget to set the global variable SUBJECTS_DIR
Cheers, Ed
On 14 Oct, 2011, at 18:00, freesurfer-request@nmr.mgh.harvard.edu wrote:
Dear Bruce and Anastasia,
Thanks for the quick reply!
I tried the bbregister as you suggested but when i visualize the target and dti image they don't look registered at all.
This is the comand i used:
bbregister --s CN01 --mov /home/joana/FA/CN01/dti_FA.nii.gz --reg /home/joana/FA/CN01/register.dat --init-fsl --dti --template-out /home/joana/FA/CN01/template.nii.gz --fslmat /home/joana/FA/CN01/ flirt.tmx
I tried to use the bbregister tools to align them but I didn't get very far...
Did i miss something?
I read in another mail something about using the register.dat created in bbregister and do mri_label2vol but i'm not sure how to do it.
Thanks,
Joana
Dear Lilla and Ed,
Thanks a lot for your suggestions, they were really really helpful!
I did the analyses as you suggested. After bbregister i checked the results with tkregister2 and saw that most subjects were well coregistered. However in a few of them my lowb images were out of place with respect to the target and so i made manual adjustments using bbregister interface tools..
I was just wondering whether this is the normal procedure as manual adjustments can be quite subjective and i would prefer not to introduce such a bias in the analyses.
Thanks a lot for your valuable help!
Joana
2011/10/15 Ed Gronenschild ed.gronenschild@np.unimaas.nl
Dear Joana,
Two things:
You should be very careful to use fslswapdim since it may result in an unintended left-right flipping. It's better to use fslreorient2std.
The tool dt-recon computes the coregistration of the lowb volume to the anatomical volume, see register.dat. You can then use the following to coregister FA:
mri_vol2vol --reg register.dat --mov fa.nii --o fa-ana.nii -targ subject/mri/T1.mgz
where "subject" is the output folder generated by the recon-all command. You should not forget to set the global variable SUBJECTS_DIR
Cheers, Ed
On 14 Oct, 2011, at 18:00, freesurfer-request@nmr.mgh.harvard.edu wrote:
Dear Bruce and Anastasia,
Thanks for the quick reply!
I tried the bbregister as you suggested but when i visualize the target and dti image they don't look registered at all.
This is the comand i used:
bbregister --s CN01 --mov /home/joana/FA/CN01/dti_FA.nii.gz --reg /home/joana/FA/CN01/register.dat --init-fsl --dti --template-out /home/joana/FA/CN01/template.nii.gz --fslmat /home/joana/FA/CN01/flirt.tmx
I tried to use the bbregister tools to align them but I didn't get very far...
Did i miss something?
I read in another mail something about using the register.dat created in bbregister and do mri_label2vol but i'm not sure how to do it.
Thanks,
Joana
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.
Even though it is not ideal, manual adjustments can be useful. I would use manual registration in a small number of cases though. If most of your data requires it, I would try to play with the automatic registration parameters more.
--Lilla
On Sun, 16 Oct 2011, Joana Braga Pereira wrote:
Dear Lilla and Ed, Thanks a lot for your suggestions, they were really really helpful!
I did the analyses as you suggested. After bbregister i checked the results with tkregister2 and saw that most subjects were well coregistered. However in a few of them my lowb images were out of place with respect to the target and so i made manual adjustments using bbregister interface tools..
I was just wondering whether this is the normal procedure as manual adjustments can be quite subjective and i would prefer not to introduce such a bias in the analyses.
Thanks a lot for your valuable help!
Joana
2011/10/15 Ed Gronenschild ed.gronenschild@np.unimaas.nl Dear Joana, Two things:
You should be very careful to use fslswapdim since it may result in an unintended left-right flipping. It's better to use fslreorient2std. 2. The tool dt-recon computes the coregistration of the lowb volume to the anatomical volume, see register.dat. You can then use the following to coregister FA:
mri_vol2vol --reg register.dat --mov fa.nii --o fa-ana.nii -targ subject/mri/T1.mgz
where "subject" is the output folder generated by the recon-all command. You should not forget to set the global variable SUBJECTS_DIR
Cheers, Ed
On 14 Oct, 2011, at 18:00, freesurfer-request@nmr.mgh.harvard.edu wrote:
Dear Bruce and Anastasia,
Thanks for the quick reply!
I tried the bbregister as you suggested but when i visualize the target and dti image they don't look registered at all.
This is the comand i used:
bbregister --s CN01 --mov /home/joana/FA/CN01/dti_FA.nii.gz --reg /home/joana/FA/CN01/register.dat --init-fsl --dti --template-out /home/joana/FA/CN01/template.nii.gz --fslmat /home/joana/FA/CN01/flirt.tmx
I tried to use the bbregister tools to align them but I didn't get very far...
Did i miss something?
I read in another mail something about using the register.dat created in bbregister and do mri_label2vol but i'm not sure how to do it.
Thanks,
Joana
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 Joana, how big were the changes that you made? Sometimes the initialization routine won't get it close enough, then bbregister fails. Can you send the bbregister log file? doug
Lilla Zollei wrote:
Even though it is not ideal, manual adjustments can be useful. I would use manual registration in a small number of cases though. If most of your data requires it, I would try to play with the automatic registration parameters more.
--Lilla
On Sun, 16 Oct 2011, Joana Braga Pereira wrote:
Dear Lilla and Ed, Thanks a lot for your suggestions, they were really really helpful!
I did the analyses as you suggested. After bbregister i checked the results with tkregister2 and saw that most subjects were well coregistered. However in a few of them my lowb images were out of place with respect to the target and so i made manual adjustments using bbregister interface tools..
I was just wondering whether this is the normal procedure as manual adjustments can be quite subjective and i would prefer not to introduce such a bias in the analyses.
Thanks a lot for your valuable help!
Joana
2011/10/15 Ed Gronenschild ed.gronenschild@np.unimaas.nl Dear Joana, Two things:
You should be very careful to use fslswapdim since it may result in an unintended left-right flipping. It's better to use fslreorient2std. 2. The tool dt-recon computes the coregistration of the lowb volume to the anatomical volume, see register.dat. You can then use the following to coregister FA:
mri_vol2vol --reg register.dat --mov fa.nii --o fa-ana.nii -targ subject/mri/T1.mgz
where "subject" is the output folder generated by the recon-all command. You should not forget to set the global variable SUBJECTS_DIR
Cheers, Ed
On 14 Oct, 2011, at 18:00, freesurfer-request@nmr.mgh.harvard.edu wrote:
Dear Bruce and Anastasia,
Thanks for the quick reply!
I tried the bbregister as you suggested but when i visualize the target and dti image they don't look registered at all.
This is the comand i used:
bbregister --s CN01 --mov /home/joana/FA/CN01/dti_FA.nii.gz --reg /home/joana/FA/CN01/register.dat --init-fsl --dti --template-out /home/joana/FA/CN01/template.nii.gz --fslmat /home/joana/FA/CN01/flirt.tmx
I tried to use the bbregister tools to align them but I didn't get very far...
Did i miss something?
I read in another mail something about using the register.dat created in bbregister and do mri_label2vol but i'm not sure how to do it.
Thanks,
Joana
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
Hi Doug,
I made quite a few changes, including translations and rotations (not scaling changes), to 10 out of 24 subjects.
Here are a few of the bbregister log.files from subjects in which the registration didn't go well.
Thanks for the help!
Joana
2011/10/17 Douglas N Greve greve@nmr.mgh.harvard.edu
Hi Joana, how big were the changes that you made? Sometimes the initialization routine won't get it close enough, then bbregister fails. Can you send the bbregister log file? doug
Lilla Zollei wrote:
Even though it is not ideal, manual adjustments can be useful. I would use manual registration in a small number of cases though. If most of your data requires it, I would try to play with the automatic registration parameters more.
--Lilla
On Sun, 16 Oct 2011, Joana Braga Pereira wrote:
Dear Lilla and Ed,
Thanks a lot for your suggestions, they were really really helpful!
I did the analyses as you suggested. After bbregister i checked the results with tkregister2 and saw that most subjects were well coregistered. However in a few of them my lowb images were out of place with respect to the target and so i made manual adjustments using bbregister interface tools..
I was just wondering whether this is the normal procedure as manual adjustments can be quite subjective and i would prefer not to introduce such a bias in the analyses.
Thanks a lot for your valuable help!
Joana
2011/10/15 Ed Gronenschild <ed.gronenschild@np.unimaas.nl**> Dear Joana, Two things:
You should be very careful to use fslswapdim since it may result in an unintended left-right flipping. It's better to use fslreorient2std. 2. The tool dt-recon computes the coregistration of the lowb volume to the anatomical volume, see register.dat. You can then use the following to coregister FA:
mri_vol2vol --reg register.dat --mov fa.nii --o fa-ana.nii -targ subject/mri/T1.mgz
where "subject" is the output folder generated by the recon-all command. You should not forget to set the global variable SUBJECTS_DIR
Cheers, Ed
On 14 Oct, 2011, at 18:00, freesurfer-request@nmr.mgh.**harvard.edufreesurfer-request@nmr.mgh.harvard.eduwrote:
Dear Bruce and Anastasia,
Thanks for the quick reply!
I tried the bbregister as you suggested but when i visualize the target and dti image they don't look registered at all.
This is the comand i used:
bbregister --s CN01 --mov /home/joana/FA/CN01/dti_FA.**nii.gz --reg /home/joana/FA/CN01/register.**dat --init-fsl --dti --template-out /home/joana/FA/CN01/template.**nii.gz --fslmat /home/joana/FA/CN01/flirt.tmx
I tried to use the bbregister tools to align them but I didn't get very far...
Did i miss something?
I read in another mail something about using the register.dat created in bbregister and do mri_label2vol but i'm not sure how to do it.
Thanks,
Joana
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://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/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Those almost surely failed because of a bad initialization. You can usually tell this by looking at the first value in the mincost file. For these, the mincost is something like .9. The mincost will be a value bet 0 and 1.1, with 0 being perfect. Looks at your good subjects to get an idea of what range to expect for well-registered subjects. You should be able to use the registrations you created as input to bbregister (with the --init-reg option), and bbregister should do fine after that. doug
Joana Braga Pereira wrote:
Hi Doug,
I made quite a few changes, including translations and rotations (not scaling changes), to 10 out of 24 subjects.
Here are a few of the bbregister log.files from subjects in which the registration didn't go well.
Thanks for the help!
Joana
2011/10/17 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
Hi Joana, how big were the changes that you made? Sometimes the initialization routine won't get it close enough, then bbregister fails. Can you send the bbregister log file? doug Lilla Zollei wrote: Even though it is not ideal, manual adjustments can be useful. I would use manual registration in a small number of cases though. If most of your data requires it, I would try to play with the automatic registration parameters more. --Lilla On Sun, 16 Oct 2011, Joana Braga Pereira wrote: Dear Lilla and Ed, Thanks a lot for your suggestions, they were really really helpful! I did the analyses as you suggested. After bbregister i checked the results with tkregister2 and saw that most subjects were well coregistered. However in a few of them my lowb images were out of place with respect to the target and so i made manual adjustments using bbregister interface tools.. I was just wondering whether this is the normal procedure as manual adjustments can be quite subjective and i would prefer not to introduce such a bias in the analyses. Thanks a lot for your valuable help! Joana 2011/10/15 Ed Gronenschild <ed.gronenschild@np.unimaas.nl <mailto:ed.gronenschild@np.unimaas.nl>> Dear Joana, Two things: 1. You should be very careful to use fslswapdim since it may result in an unintended left-right flipping. It's better to use fslreorient2std. 2. The tool dt-recon computes the coregistration of the lowb volume to the anatomical volume, see register.dat. You can then use the following to coregister FA: mri_vol2vol --reg register.dat --mov fa.nii --o fa-ana.nii -targ subject/mri/T1.mgz where "subject" is the output folder generated by the recon-all command. You should not forget to set the global variable SUBJECTS_DIR Cheers, Ed On 14 Oct, 2011, at 18:00, freesurfer-request@nmr.mgh.harvard.edu <mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote: Dear Bruce and Anastasia, Thanks for the quick reply! I tried the bbregister as you suggested but when i visualize the target and dti image they don't look registered at all. This is the comand i used: bbregister --s CN01 --mov /home/joana/FA/CN01/dti_FA.nii.gz --reg /home/joana/FA/CN01/register.dat --init-fsl --dti --template-out /home/joana/FA/CN01/template.nii.gz --fslmat /home/joana/FA/CN01/flirt.tmx I tried to use the bbregister tools to align them but I didn't get very far... Did i miss something? I read in another mail something about using the register.dat created in bbregister and do mri_label2vol but i'm not sure how to do it. Thanks, Joana _______________________________________________ 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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Hi Doug,
Thanks for the reply. I'm not sure i understand how to solve it. Are you suggesting to re-run bbregister using the --init-reg option and the register.dat files that were previously created for the badly-registered subjects?
Joana
2011/10/17 Douglas N Greve greve@nmr.mgh.harvard.edu
Those almost surely failed because of a bad initialization. You can usually tell this by looking at the first value in the mincost file. For these, the mincost is something like .9. The mincost will be a value bet 0 and 1.1, with 0 being perfect. Looks at your good subjects to get an idea of what range to expect for well-registered subjects. You should be able to use the registrations you created as input to bbregister (with the --init-reg option), and bbregister should do fine after that. doug
Joana Braga Pereira wrote:
Hi Doug,
I made quite a few changes, including translations and rotations (not scaling changes), to 10 out of 24 subjects.
Here are a few of the bbregister log.files from subjects in which the registration didn't go well.
Thanks for the help!
Joana
2011/10/17 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>>
Hi Joana, how big were the changes that you made? Sometimes the initialization routine won't get it close enough, then bbregister fails. Can you send the bbregister log file? doug
Lilla Zollei wrote:
Even though it is not ideal, manual adjustments can be useful. I would use manual registration in a small number of cases though. If most of your data requires it, I would try to play with the automatic registration parameters more. --Lilla On Sun, 16 Oct 2011, Joana Braga Pereira wrote: Dear Lilla and Ed, Thanks a lot for your suggestions, they were really really helpful! I did the analyses as you suggested. After bbregister i checked the results with tkregister2 and saw that most subjects were well coregistered. However in a few of them my lowb images were out of place with respect to the target and so i made manual adjustments using bbregister interface tools.. I was just wondering whether this is the normal procedure as manual adjustments can be quite subjective and i would prefer not to introduce such a bias in the analyses. Thanks a lot for your valuable help! Joana 2011/10/15 Ed Gronenschild <ed.gronenschild@np.unimaas.nl <mailto:ed.gronenschild@np.**unimaas.nled.gronenschild@np.unimaas.nl
Dear Joana, Two things: 1. You should be very careful to use fslswapdim since it may result in an unintended left-right flipping. It's better to use fslreorient2std. 2. The tool dt-recon computes the coregistration of the lowb volume to the anatomical volume, see register.dat. You can then use the following to coregister FA: mri_vol2vol --reg register.dat --mov fa.nii --o fa-ana.nii -targ subject/mri/T1.mgz where "subject" is the output folder generated by the recon-all command. You should not forget to set the global variable SUBJECTS_DIR Cheers, Ed On 14 Oct, 2011, at 18:00, freesurfer-request@nmr.mgh.**harvard.edu<freesurfer-request@nmr.mgh.harvard.edu> <mailto:freesurfer-request@**nmr.mgh.harvard.edu<freesurfer-request@nmr.mgh.harvard.edu>>wrote:
Dear Bruce and Anastasia, Thanks for the quick reply! I tried the bbregister as you suggested but when i visualize the target and dti image they don't look registered at all. This is the comand i used: bbregister --s CN01 --mov /home/joana/FA/CN01/dti_FA.**nii.gz --reg /home/joana/FA/CN01/register.**dat --init-fsl --dti --template-out /home/joana/FA/CN01/template.**nii.gz --fslmat /home/joana/FA/CN01/flirt.tmx I tried to use the bbregister tools to align them but I didn't get very far... Did i miss something? I read in another mail something about using the register.dat created in bbregister and do mri_label2vol but i'm not sure how to do it. Thanks, Joana ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer 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<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 <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
No, use the register.dat that you manually created as the input to bbregister with the --init-reg. You could move your register.dat to regidster.man.dat and set the output to be register.dat. doug
Joana Braga Pereira wrote:
Hi Doug,
Thanks for the reply. I'm not sure i understand how to solve it. Are you suggesting to re-run bbregister using the --init-reg option and the register.dat files that were previously created for the badly-registered subjects?
Joana
2011/10/17 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
Those almost surely failed because of a bad initialization. You can usually tell this by looking at the first value in the mincost file. For these, the mincost is something like .9. The mincost will be a value bet 0 and 1.1, with 0 being perfect. Looks at your good subjects to get an idea of what range to expect for well-registered subjects. You should be able to use the registrations you created as input to bbregister (with the --init-reg option), and bbregister should do fine after that. doug Joana Braga Pereira wrote: Hi Doug, I made quite a few changes, including translations and rotations (not scaling changes), to 10 out of 24 subjects. Here are a few of the bbregister log.files from subjects in which the registration didn't go well. Thanks for the help! Joana 2011/10/17 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> Hi Joana, how big were the changes that you made? Sometimes the initialization routine won't get it close enough, then bbregister fails. Can you send the bbregister log file? doug Lilla Zollei wrote: Even though it is not ideal, manual adjustments can be useful. I would use manual registration in a small number of cases though. If most of your data requires it, I would try to play with the automatic registration parameters more. --Lilla On Sun, 16 Oct 2011, Joana Braga Pereira wrote: Dear Lilla and Ed, Thanks a lot for your suggestions, they were really really helpful! I did the analyses as you suggested. After bbregister i checked the results with tkregister2 and saw that most subjects were well coregistered. However in a few of them my lowb images were out of place with respect to the target and so i made manual adjustments using bbregister interface tools.. I was just wondering whether this is the normal procedure as manual adjustments can be quite subjective and i would prefer not to introduce such a bias in the analyses. Thanks a lot for your valuable help! Joana 2011/10/15 Ed Gronenschild <ed.gronenschild@np.unimaas.nl <mailto:ed.gronenschild@np.unimaas.nl> <mailto:ed.gronenschild@np.unimaas.nl <mailto:ed.gronenschild@np.unimaas.nl>>> Dear Joana, Two things: 1. You should be very careful to use fslswapdim since it may result in an unintended left-right flipping. It's better to use fslreorient2std. 2. The tool dt-recon computes the coregistration of the lowb volume to the anatomical volume, see register.dat. You can then use the following to coregister FA: mri_vol2vol --reg register.dat --mov fa.nii --o fa-ana.nii -targ subject/mri/T1.mgz where "subject" is the output folder generated by the recon-all command. You should not forget to set the global variable SUBJECTS_DIR Cheers, Ed On 14 Oct, 2011, at 18:00, freesurfer-request@nmr.mgh.harvard.edu <mailto:freesurfer-request@nmr.mgh.harvard.edu> <mailto:freesurfer-request@nmr.mgh.harvard.edu <mailto:freesurfer-request@nmr.mgh.harvard.edu>> wrote: Dear Bruce and Anastasia, Thanks for the quick reply! I tried the bbregister as you suggested but when i visualize the target and dti image they don't look registered at all. This is the comand i used: bbregister --s CN01 --mov /home/joana/FA/CN01/dti_FA.nii.gz --reg /home/joana/FA/CN01/register.dat --init-fsl --dti --template-out /home/joana/FA/CN01/template.nii.gz --fslmat /home/joana/FA/CN01/flirt.tmx I tried to use the bbregister tools to align them but I didn't get very far... Did i miss something? I read in another mail something about using the register.dat created in bbregister and do mri_label2vol but i'm not sure how to do it. Thanks, Joana _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Thanks Doug! It worked!
Joana
2011/10/17 Douglas N Greve greve@nmr.mgh.harvard.edu
No, use the register.dat that you manually created as the input to bbregister with the --init-reg. You could move your register.dat to regidster.man.dat and set the output to be register.dat.
doug
Joana Braga Pereira wrote:
Hi Doug,
Thanks for the reply. I'm not sure i understand how to solve it. Are you suggesting to re-run bbregister using the --init-reg option and the register.dat files that were previously created for the badly-registered subjects?
Joana
2011/10/17 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>>
Those almost surely failed because of a bad initialization. You can usually tell this by looking at the first value in the mincost file. For these, the mincost is something like .9. The mincost will be a value bet 0 and 1.1, with 0 being perfect. Looks at your good subjects to get an idea of what range to expect for well-registered subjects. You should be able to use the registrations you created as input to bbregister (with the --init-reg option), and bbregister should do fine after that. doug
Joana Braga Pereira wrote:
Hi Doug, I made quite a few changes, including translations and rotations (not scaling changes), to 10 out of 24 subjects. Here are a few of the bbregister log.files from subjects in which the registration didn't go well. Thanks for the help! Joana 2011/10/17 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>>> Hi Joana, how big were the changes that you made? Sometimes the initialization routine won't get it close enough, then bbregister fails. Can you send the bbregister log file? doug Lilla Zollei wrote: Even though it is not ideal, manual adjustments can be useful. I would use manual registration in a small number of cases though. If most of your data requires it, I would try to play with the automatic registration parameters more. --Lilla On Sun, 16 Oct 2011, Joana Braga Pereira wrote: Dear Lilla and Ed, Thanks a lot for your suggestions, they were really really helpful! I did the analyses as you suggested. After bbregister i checked the results with tkregister2 and saw that most subjects were well coregistered. However in a few of them my lowb images were out of place with respect to the target and so i made manual adjustments using bbregister interface tools.. I was just wondering whether this is the normal procedure as manual adjustments can be quite subjective and i would prefer not to introduce such a bias in the analyses. Thanks a lot for your valuable help! Joana 2011/10/15 Ed Gronenschild <ed.gronenschild@np.unimaas.nl <mailto:ed.gronenschild@np.**unimaas.nl<ed.gronenschild@np.unimaas.nl><mailto:ed.gronenschild@np.**unimaas.nl<ed.gronenschild@np.unimaas.nl> <mailto:ed.gronenschild@np.**unimaas.nl<ed.gronenschild@np.unimaas.nl>Dear Joana, Two things: 1. You should be very careful to use fslswapdim since it may result in an unintended left-right flipping. It's better to use fslreorient2std. 2. The tool dt-recon computes the coregistration of the lowb volume to the anatomical volume, see register.dat. You can then use the following to coregister FA: mri_vol2vol --reg register.dat --mov fa.nii --o fa-ana.nii -targ subject/mri/T1.mgz where "subject" is the output folder generated by the recon-all command. You should not forget to set the global variable SUBJECTS_DIR Cheers, Ed On 14 Oct, 2011, at 18:00, freesurfer-request@nmr.mgh.**harvard.edu<freesurfer-request@nmr.mgh.harvard.edu> <mailto:freesurfer-request@**nmr.mgh.harvard.edu<freesurfer-request@nmr.mgh.harvard.edu><mailto:freesurfer-request@**nmr.mgh.harvard.edu<freesurfer-request@nmr.mgh.harvard.edu> <mailto:freesurfer-request@**nmr.mgh.harvard.edu<freesurfer-request@nmr.mgh.harvard.edu>>>wrote:
Dear Bruce and Anastasia, Thanks for the quick reply! I tried the bbregister as you suggested but when i visualize the target and dti image they don't look registered at all. This is the comand i used: bbregister --s CN01 --mov /home/joana/FA/CN01/dti_FA.**nii.gz --reg /home/joana/FA/CN01/register.**dat --init-fsl --dti --template-out /home/joana/FA/CN01/template.**nii.gz --fslmat /home/joana/FA/CN01/flirt.tmx I tried to use the bbregister tools to align them but I didn't get very far... Did i miss something? I read in another mail something about using the register.dat created in bbregister and do mri_label2vol but i'm not sure how to do it. Thanks, Joana ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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<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. ------------------------------**------------------------------**------------
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting><http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html><http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Ed Gronenschild -
Joana Braga Pereira -
Lilla Zollei