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Hi Freesurfer Team, How may I align 5 volumes of my PET data ( 5 min acquisitions each) to a mean image for motion correction across the acquisition? I can use mri_concat to get the the mean image, but I am not sure how to do the realignment after that. Thank you. Best Wishes,Shane
If you have them in nifti format, you can use afni or fsl (we don't have our own motion correction)
On 5/3/2019 1:18 PM, Shane Schofield wrote:
External Email - Use Caution
Hi Freesurfer Team,
How may I align 5 volumes of my PET data ( 5 min acquisitions each) to a mean image for motion correction across the acquisition? I can use mri_concat to get the the mean image, but I am not sure how to do the realignment after that.
Thank you.
Best Wishes, Shane
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Thanks, Doug. I think the command is MCFLIRT. https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MCFLIRT
Best Wishes,Shane On Friday, May 3, 2019, 6:18:54 PM GMT+1, Shane Schofield shane.schofield@yahoo.com wrote:
Hi Freesurfer Team, How may I align 5 volumes of my PET data ( 5 min acquisitions each) to a mean image for motion correction across the acquisition? I can use mri_concat to get the the mean image, but I am not sure how to do the realignment after that. Thank you. Best Wishes,Shane
freesurfer@nmr.mgh.harvard.edu
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Greve, Douglas N.,Ph.D. -
Shane Schofield