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Hello FreeSurfer Developers,
I am attempting to run recon-all on a group of subjects. We no longer have the raw T1s. Instead, we have their orig.mgz and T1.mgz files from a previous run of freesurfer. We wish to rerun recon-all using their orig.mgz or T1.mgz as inputs, using FreeSurfer5.3. What would be the best way to go about this?
1. I ran recon-all normally, with orig.mgz as the input file. It ran to completion, but some files are missing from subdirectories. I am not sure if the outputs are correct, and comparable to other datasets that have freesurfer outputs that used raw T1s.
2. I converted orig.mgz to orig.nii.gz using mri_convert, and used orig.nii.gz as input to recon-all. This also ran to completion. However, because I cannot compare this output to any "true" output, I am unsure if the outputs are correct, and is the same as using a raw T1 as input.
3. I considered manually starting the recon process from T1.mgz (organizing subdirectories manually, inserting T1.mgz and orig.mgz into /mri, and starting autorecon2. I am unsure if this is best, as I am missing nu.mgz, which is an input file in the first step of autorecon2.
Please let me know what you think, and which method you think would be closest to using the raw T1s. I've searched the list and it seems that no one has attempted a similar task. Thank you.
Sincerely, Melody