You'll need to register the PET data to the anatomical. Make an mean
image of all the frames
mri_concat tac.nii.gz --mean --o mean.tac.nii.gz
Then run bbregister using the mean.tac.nii.gz as the mov, specify --t2
as the weighting
doug
On 6/30/15 10:33 AM, Rodriguez-Thompson, Anais wrote:
Hi freesurfer experts,
We are analyzing data from a simultaneous PET-MRI study, and are having
problems overlaying BPnd volume files onto our subjects' volume space. I've
attached an image of the issue-- it seems as if the BPnd image is shifted
towards the left of the subject's brain.
Our BPnd volume files were given to us by the center's PET team. The file
pathway is
/cluster/roffman/users/Stable5_PerRun/NNC_PMOD_LoganRef_BPnd/fs_NNC112_0078_RBV_MC_s10v3_LoganRef_BPnd.nii
Once we cd into the folder
/cluster/roffman/users/Stable5_PerRun/NNC_PMOD_LoganRef_BPnd/ the command we
are using is
tkmedit NNC0078 orig.mgz -overlay fs_NNC112_0078_RBV_MC_s10v3_LoganRef_BPnd.nii
There have been several more subjects that have shown the same registration
issues. Is there a way to correct for this automatically through freesurfer? If
so, what steps should we add to our commands to be able to do so?
Thank you for your help!
Anais
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