Hi all,
We're trying to use FLAIR images in our recon-all pipeline. For half of the participants there are no problems using: recon-all -subjid SUBJECT -i T1.nii -all -FLAIR FLAIR.nii -FLAIRpial
However for the other half the FLAIR registrations are either a bit off or completely flipped, including swapping axes. This then affects the generate surfaces.
The problem line seems to be: bbregister --s <subjid> --mov mri/orig/FLAIRraw.mgz --lta mri/transforms/FLAIRraw.lta --init-fsl --T2
as the output registration of these files is incorrect.
We've tried using mri_convert instead of dcm2nii. This does not solve the problem. Loading the FLAIR.nii in fslview, the image is upside down, but the letters indicating orientation are correct.
Do you have any suggestions about how to solve this problem?
Thanks, Konrad
can you try --init-spm instead of --init-fsl and see if it does better? On Mon, 22 Feb 2016, K. Wagstyl wrote:
Hi all,
We're trying to use FLAIR images in our recon-all pipeline. For half of the participants there are no problems using: recon-all -subjid SUBJECT -i T1.nii -all -FLAIR FLAIR.nii -FLAIRpial
However for the other half the FLAIR registrations are either a bit off or completely flipped, including swapping axes. This then affects the generate surfaces.
The problem line seems to be: bbregister --s <subjid> --mov mri/orig/FLAIRraw.mgz --lta mri/transforms/FLAIRraw.lta --init-fsl --T2
as the output registration of these files is incorrect.
We've tried using mri_convert instead of dcm2nii. This does not solve the problem. Loading the FLAIR.nii in fslview, the image is upside down, but the letters indicating orientation are correct.
Do you have any suggestions about how to solve this problem?
Thanks, Konrad _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
--init-spm works much better thanks. Is there a way to rerun autorecon3 using --init-spm rather than --init-fsl?
Or do we need to run the commands line by line.
Cheers, Konrad
On 2016-02-22 13:45, Bruce Fischl wrote:
can you try --init-spm instead of --init-fsl and see if it does better? On Mon, 22 Feb 2016, K. Wagstyl wrote:
Hi all,
We're trying to use FLAIR images in our recon-all pipeline. For half of the participants there are no problems using: recon-all -subjid SUBJECT -i T1.nii -all -FLAIR FLAIR.nii -FLAIRpial
However for the other half the FLAIR registrations are either a bit off or completely flipped, including swapping axes. This then affects the generate surfaces.
The problem line seems to be: bbregister --s <subjid> --mov mri/orig/FLAIRraw.mgz --lta mri/transforms/FLAIRraw.lta --init-fsl --T2
as the output registration of these files is incorrect.
We've tried using mri_convert instead of dcm2nii. This does not solve the problem. Loading the FLAIR.nii in fslview, the image is upside down, but the letters indicating orientation are correct.
Do you have any suggestions about how to solve this problem?
Thanks, Konrad _______________________________________________ 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
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not sure. Doug? On Mon, 22 Feb 2016, K. Wagstyl wrote:
Hi Bruce,
--init-spm works much better thanks. Is there a way to rerun autorecon3 using --init-spm rather than --init-fsl?
Or do we need to run the commands line by line.
Cheers, Konrad
On 2016-02-22 13:45, Bruce Fischl wrote:
can you try --init-spm instead of --init-fsl and see if it does better? On Mon, 22 Feb 2016, K. Wagstyl wrote:
Hi all,
We're trying to use FLAIR images in our recon-all pipeline. For half of the participants there are no problems using: recon-all -subjid SUBJECT -i T1.nii -all -FLAIR FLAIR.nii -FLAIRpial
However for the other half the FLAIR registrations are either a bit off or completely flipped, including swapping axes. This then affects the generate surfaces.
The problem line seems to be: bbregister --s <subjid> --mov mri/orig/FLAIRraw.mgz --lta mri/transforms/FLAIRraw.lta --init-fsl --T2
as the output registration of these files is incorrect.
We've tried using mri_convert instead of dcm2nii. This does not solve the problem. Loading the FLAIR.nii in fslview, the image is upside down, but the letters indicating orientation are correct.
Do you have any suggestions about how to solve this problem?
Thanks, Konrad _______________________________________________ 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
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
K. Wagstyl