the problem is,, when you re-run the base with different images, it will create the median image at a different location. That means that all your edits will be at the wrong location. I currently don’t see a way to fix this easily without a lot of tweaking of the recon-all script. One potential approach could be to manually create the new template with the correct images at the same location as before, by passing the old template into the mri_robust_template code as an initial target (not even sure there is a flag for that). Then start recon-all from a later stage after that. I cannot support you for this and it requires some coding skills and good knowledge of the individual steps in the base pipeline.

On 31. Jul 2018, at 18:35, KALEY E ELLIS <keedwards2@wisc.edu> wrote:

Dear FreeSurfer Developers,

I posted this question last week, but did not receive a response. Please let me know if I can provide any additional information.

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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer