External Email - Use Caution Hello,
Thank you for your response. I am not trying to preserve previous recon-all outputs, because the only outputs I have from the previous run are the orig.mgz and T1.mgz files. Can I use your commands above, except with the orig.mgz file, not the 00x.mgz file? If not, which options would you suggest that would get me closest to the output I would have gotten if I did have the raw T1s? Thank you, Melody On Thu, Mar 21, 2024 at 4:51 AM Huang, Yujing <yhuan...@mgh.harvard.edu> wrote: > 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. 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If you do not > wish to continue communication over unencrypted e-mail, please notify the > sender of this message immediately. Continuing to send or respond to > e-mail after receiving this message means you understand and accept this > risk and wish to continue to communicate over unencrypted e-mail. > -- *Melody Jeong Yeon Kang* Ph.D. Student Imaging Genetics Center *USC* Stevens Neuroimaging and Informatics Institute Keck School of Medicine of *USC* University of Southern California Email: jkang...@usc.edu
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