Dear List,
I have a question regarding using .img in Freesurfer.
We only have analyze images, but we can tell the orientation of the images through the patient's lesion location. Because freesurfer sometimes flips these image after recon-all, I'm now flipping the "problematic" ones using mri_convert <input> --out_orientation RAS <output> before running them again.
Could someone please explain why if we use analyze images, some of them would be flipped by Freesurfer but not others? Does that only apply to lesioned/patient brains and not normal brains?
Many thanks! Catherine
Dear Catherine I think freesurfer uses the voxel space not world space (hdr file). some other programs use hdr file too which means world space like spm. if you want to have same world space and voxel space you have to have re-slice your img file in spm if you use spm. then everything would be same in every program.
Best Rouhi
On Thu, Aug 11, 2011 at 4:34 PM, Catherine Wan cycwan@gmail.com wrote:
Dear List,
I have a question regarding using .img in Freesurfer.
We only have analyze images, but we can tell the orientation of the images through the patient's lesion location. Because freesurfer sometimes flips these image after recon-all, I'm now flipping the "problematic" ones using mri_convert <input> --out_orientation RAS <output> before running them again.
Could someone please explain why if we use analyze images, some of them would be flipped by Freesurfer but not others? Does that only apply to lesioned/patient brains and not normal brains?
Many thanks! Catherine
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.
no, we use the info in the .hdr file. The problem is that there just isn't enough there to figure out the direction cosines. That was one of the big motivations for creating nifti
Bruce
On Thu, 11 Aug 2011, Rouhollah Abdollahi wrote:
Dear Catherine I think freesurfer uses the voxel space not world space (hdr file). some other programs use hdr file too which means world space like spm. if you want to have same world space and voxel space you have to have re-slice your img file in spm if you use spm. then everything would be same in every program.
Best Rouhi
On Thu, Aug 11, 2011 at 4:34 PM, Catherine Wan cycwan@gmail.com wrote: Dear List,
I have a question regarding using .img in Freesurfer. We only have analyze images, but we can tell the orientation of the images through the patient's lesion location. Because freesurfer sometimes flips these image after recon-all, I'm now flipping the "problematic" ones using mri_convert <input> --out_orientation RAS <output> before running them again. Could someone please explain why if we use analyze images, some of them would be flipped by Freesurfer but not others? Does that only apply to lesioned/patient brains and not normal brains? Many thanks! Catherine _______________________________________________ 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.-- With Best Regards Rouhollah Abdollahi
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Catherine Wan -
Rouhollah Abdollahi