Not sure what went wrong in your previous run. Do you have ‘mri/orig’ directory
under $SUBJECTS_DIR/subj? Do you have 00x.mgz in that directory?
Re-run with ‘orig.mgz’ is fine. You probably need to name the subject
differently.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Jeong Yeon Kang
Sent: Thursday, March 21, 2024 2:04 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Using orig.mgz or T1.mgz as input to recon-all
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<mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto: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<mailto: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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be
https://urldefense.com/v3/__https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer__;!!LIr3w8kk_Xxm!suC0ljDaaQQaB17fugf4TQLVHrdm-12K67Y9RxXdLx143EfGT1s9PrR-BDgZMdRAapOgch1GScoyi3JMtdgXQY_CgqU$<https://secure-web.cisco.com/1sTD8PKMK4Bfs6yysf4UyD7ISy_6-kbnP3D8hbuLxvd3B7PcJAU4ewcUySOW7LMWMPMWMDZawJbAgbOwBk8uG_V67v7zFT6zFmXVe0j0T9g_EYx_yvW3VKt5BC57yMBuY6Ojic0hwxo1JmPdCUzAeZBo8xajvKYLw7c7zSgEuZgYwmttDhQWZgXtRMvnU9obqlpVdLdj_GnTf4d68YkWsKwlKH4-QiB0UYIUGq0E6rnedT0sG_QUJ0758w_x8YBE7pFtNdgjaUmMYM4gt3MDpjk8X_HsFNPRlhXJ7zd9CPnU3d3__-sZpwRac1JsWD3JmPnH9hpQDHK0_Z_O9bwWxfw/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__%3B%21%21LIr3w8kk_Xxm%21suC0ljDaaQQaB17fugf4TQLVHrdm-12K67Y9RxXdLx143EfGT1s9PrR-BDgZMdRAapOgch1GScoyi3JMtdgXQY_CgqU%24>
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be
https://urldefense.com/v3/__https://www.massgeneralbrigham.org/complianceline__;!!LIr3w8kk_Xxm!suC0ljDaaQQaB17fugf4TQLVHrdm-12K67Y9RxXdLx143EfGT1s9PrR-BDgZMdRAapOgch1GScoyi3JMtdgXkBK31Ys$<https://secure-web.cisco.com/13DVcqMHglKy7J9IPOiukQP2tdR8VCrcprrDa6vASf8_hPy6UXSg7hd6Qf953dS68mfRik5RJQrvTApeAxY1RrJD1B6kS_hxzABvJZPhski6CL9K66l0snBPDFbQfyOvAmPNVJvFQWMyBRy9YS07-6yPgKvO44NYXkC3ZGT8golkO1ndKvVgWeOSUZY66bWavTykKSlwIZJrhGfAojME31Q-6MZgXzYmfOw2WRq92FGtYcc3c6Z1prItSKg5GnxZawe0122NlRhDue5szaqQMmcJoiFBBbgoIRzvvMpRpXd6mHQvFSZTakp1to9KMGtr2Du0tK9_SlCOun9gcidSflQ/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline__%3B%21%21LIr3w8kk_Xxm%21suC0ljDaaQQaB17fugf4TQLVHrdm-12K67Y9RxXdLx143EfGT1s9PrR-BDgZMdRAapOgch1GScoyi3JMtdgXkBK31Ys%24>
<MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be
https://urldefense.com/v3/__https://www.massgeneralbrigham.org/complianceline__;!!LIr3w8kk_Xxm!suC0ljDaaQQaB17fugf4TQLVHrdm-12K67Y9RxXdLx143EfGT1s9PrR-BDgZMdRAapOgch1GScoyi3JMtdgXkBK31Ys$<https://secure-web.cisco.com/13DVcqMHglKy7J9IPOiukQP2tdR8VCrcprrDa6vASf8_hPy6UXSg7hd6Qf953dS68mfRik5RJQrvTApeAxY1RrJD1B6kS_hxzABvJZPhski6CL9K66l0snBPDFbQfyOvAmPNVJvFQWMyBRy9YS07-6yPgKvO44NYXkC3ZGT8golkO1ndKvVgWeOSUZY66bWavTykKSlwIZJrhGfAojME31Q-6MZgXzYmfOw2WRq92FGtYcc3c6Z1prItSKg5GnxZawe0122NlRhDue5szaqQMmcJoiFBBbgoIRzvvMpRpXd6mHQvFSZTakp1to9KMGtr2Du0tK9_SlCOun9gcidSflQ/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline__%3B%21%21LIr3w8kk_Xxm%21suC0ljDaaQQaB17fugf4TQLVHrdm-12K67Y9RxXdLx143EfGT1s9PrR-BDgZMdRAapOgch1GScoyi3JMtdgXkBK31Ys%24>
> .
Please note that this e-mail is not secure (encrypted). 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<mailto:jkang...@usc.edu>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). 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.
