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Dear FreeSurfer Developers,
We are using your longitudinal processing pipeline (version 6.0) for our study (n=140, 3 timepoints). Our scanner was upgraded a year ago and the a filter was used on the raw images to adjust for hyperintensities in the images due to using a multi-channel coil.
At this point, our bases have already been processed and consist of three timepoints with a mix of filters: T1 no filter, T2 no filter, T3 with filter. Since we have invested many resources into the manual editing process, we want to try to retain all the manual edits that have been done to the base. We still have the original scan and the filtered scan for each subject. We have some ideas on how we might be able to retain the edits, but would you be able to provide input regarding whether this seems reasonable? Your feedback is greatly appreciated!
Plan A: 1) Create a new T3 cross-sectional with the correct nifti 2) Run recon-all on the existing base Q: Will this retain the previous manual edits AND incorporate the new cross-sectional image?
Plan B: 1) Create a new T3 cross-sectional with the correct nifti 2) Create a new base Q: Is it possible to transfer data from old manual edits to a new base? If so, how?
Thank you! Kaley
Associate Research Specialist Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison