Are you trying to preserve previous recon-all output and re-run using different
version of Freesurfer?
If not, ‘recon-all -all -s <subjid>’ will re-run recon-all from the beginning.
You can find the original input to recon-all in mri/orig/00x.mgz. You can also
construct new subject directory structure by copying mri/orig/00x.mgz, and run
‘recon-all -all -s <subjid>’.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Jeong Yeon Kang
Sent: Wednesday, March 20, 2024 6:20 PM
To: Freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Using orig.mgz or T1.mgz as input to recon-all
External Email - Use Caution
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
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