I had one more question: What transform do I apply to get all the norm.mgz of all timepoints of a subject to get the normalized image in MNI atlas space. Is this the one inside mri/transforms/talairach.xfm? More precisely, for all subjects, will something like this work? mri_convert norm.mgz normInMNI.img --apply_transform transforms/talairach.xfm -oc 0 0 0 -oni 256 -onj 256 -onk 256 -vs 1.0 1.0 1.0 --out_data_type float"
Thanks, Prasanna
On Thu, Dec 13, 2012 at 10:30 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
Hi Prasanna, the norm.mgz sounds like the best fit. Though I'm not sure what you mean by all the images registered to the 1st time point. If you are doing a longitudinal analysis, then following the longitudinal stream will result in a set of norm.mgz's that will be in alignment (but not to the 1st time point, which you would not want because it causes bias). doug
On 12/13/2012 12:28 PM, Prasanna M wrote:
I ran Freesurfer on OASIS longitudinal data with the longitudinal pipeline. I want to work with the full brain image (with gray level intensities) which is intensity normalized and skull stripped and all the timepoints of a subject are rigidly registered to the 1st time point. There were many brain mgz files created during the processing. What is the best final image which I should be working with?
Thanks, Prasanna
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