Hi Noam, sorry, this one slipped through the cracks (would not have seen it except for Chris' email today). The problem with your data is not that the brain is upside down but that the letters (AP, LR, SI) are not appropriate. I just tried this procedure on my data and could not replicate this problem. When you load the brainmask.nii.gz into fslview, are the letters still wrong? What was the flirt command line that ApplyXFM generated? doug
On 09/06/2011 05:23 PM, noam Schneck wrote: > Dear FS experts, > > I'm sorry to pester but I am still having trouble trying to integrate > registration matrices produced by BBR into my FSL processing stream. I > ran BBR on a subject that I had run Recon-all for. I used BBR to > register the example_func.nii.gz to the bert/mri/orig.mgz. I had BBR > output an fsl.mat. I then used ApplyXFM in fsl to apply BBR's fsl.mat > to register the example_func.nii.gz onto a T1 image that had been > created by converting bert/mri/brainmask.mgz into niftii with > mri_convert. I tried it again, this time converting the orig.mgz to > niftii. In both cases the example_func in T1 space image produced by > ApplyXFM is rotated about 90 degrees and also inverted. I've attached > a screenchot from fslview. > > > Thank you for your help, > Noam -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ 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.
