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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
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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
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 YHUANG43@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-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@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?
- 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.
- 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.
- 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
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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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 <YHUANG43@mgh.harvard.edumailto:YHUANG43@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Jeong Yeon Kang Sent: Wednesday, March 20, 2024 6:20 PM To: Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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/listinf...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/compliancelin...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/compliancelin...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: jkang395@usc.edumailto:jkang395@usc.edu
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Ah - I should have clarified that the files we have are from a collaborator. They ran the previous FreeSurfer run. They gave us only the orig.mgz and T1.mgz files - so we don't have any of the mri/orig files, or any other directories. Just the two mgz files.
Thank you for clarifying that I can use the orig.mgz files as input, and I'll use the "recon-all -all -s <subjid>" command. Please let me know if there is anything I should change/ watch out for!
Thank you, Melody
On Fri, Mar 22, 2024 at 5:03 AM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:
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-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@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 YHUANG43@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-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@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?
- 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.
- 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.
- 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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*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: jkang395@usc.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
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Huang, Yujing -
Jeong Yeon Kang