External Email - Use Caution
*Hello Freesurfer Developers*
recon-all is shutting down for some reason, this is the last lines of the code before shutting down. (It ran approximately 11-12 hours)
and fyi = I used flair image because there was no T1 image of the patient [image: image.png]
and this is the log file (recon-all.log) = [image: image.png]
Can you attach the log file. I can't read the pics you attached
On 6/18/2024 10:56 AM, egemen gok wrote:
External Email - Use Caution
*Hello Freesurfer Developers*
recon-all is shutting down for some reason, this is the last lines of the code before shutting down. (It ran approximately 11-12 hours)
and fyi = I used flair image because there was no T1 image of the patient
image.png
and this is the log file (recon-all.log) =
image.png
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thank you for your response. Okay, one more update. I tried recon-all for patients with T1. Unfortunately it doesnt work for my specific dataset. Neither functions like 5ttgen does not work from MRTrix.
I need to process this dataset for a huge study of our faculty. I hope we can fix this.
Kind regards Egemen
Douglas N. Greve dgreve@mgh.harvard.edu, 24 Haz 2024 Pzt, 16:48 tarihinde şunu yazdı:
Can you attach the log file. I can't read the pics you attached
On 6/18/2024 10:56 AM, egemen gok wrote:
External Email - Use Caution*Hello Freesurfer Developers*
recon-all is shutting down for some reason, this is the last lines of the code before shutting down. (It ran approximately 11-12 hours)
and fyi = I used flair image because there was no T1 image of the patient [image: image.png]
and this is the log file (recon-all.log) = [image: image.png]
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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%3E .
You have an "extra large" defect that you will probably have to fix by hand. See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freev...
On 6/24/2024 12:42 PM, egemen gok wrote:
External Email - Use Caution
Thank you for your response. Okay, one more update. I tried recon-all for patients with T1. Unfortunately it doesnt work for my specific dataset. Neither functions like 5ttgen does not work from MRTrix.
I need to process this dataset for a huge study of our faculty. I hope we can fix this.
Kind regards Egemen
Douglas N. Greve dgreve@mgh.harvard.edu, 24 Haz 2024 Pzt, 16:48 tarihinde şunu yazdı:
Can you attach the log file. I can't read the pics you attached On 6/18/2024 10:56 AM, egemen gok wrote:External Email - Use Caution *Hello Freesurfer Developers* recon-all is shutting down for some reason, this is the last lines of the code before shutting down. (It ran approximately 11-12 hours) and fyi = I used flair image because there was no T1 image of the patient image.png and this is the log file (recon-all.log) = image.png _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ 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> .
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
My subjects have pathological tissues, is it fixable by your method?
[image: image.png]
Douglas N. Greve dgreve@mgh.harvard.edu, 28 Haz 2024 Cum, 16:25 tarihinde şunu yazdı:
You have an "extra large" defect that you will probably have to fix by hand. See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freev...
On 6/24/2024 12:42 PM, egemen gok wrote:
External Email - Use CautionThank you for your response. Okay, one more update. I tried recon-all for patients with T1. Unfortunately it doesnt work for my specific dataset. Neither functions like 5ttgen does not work from MRTrix.
I need to process this dataset for a huge study of our faculty. I hope we can fix this.
Kind regards Egemen
Douglas N. Greve dgreve@mgh.harvard.edu, 24 Haz 2024 Pzt, 16:48 tarihinde şunu yazdı:
Can you attach the log file. I can't read the pics you attached
On 6/18/2024 10:56 AM, egemen gok wrote:
External Email - Use Caution*Hello Freesurfer Developers*
recon-all is shutting down for some reason, this is the last lines of the code before shutting down. (It ran approximately 11-12 hours)
and fyi = I used flair image because there was no T1 image of the patient [image: image.png]
and this is the log file (recon-all.log) = [image: image.png]
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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%3E .
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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%3E .
External Email - Use Caution
And btw the result of my recon-all is so terrible, I tried your method but it says lh.white is not loadable. In this situation, is it fixable when it has this much defect
[image: image.png]
egemen gok egemen4552@gmail.com, 29 Haz 2024 Cmt, 05:22 tarihinde şunu yazdı:
My subjects have pathological tissues, is it fixable by your method?
[image: image.png]
Douglas N. Greve dgreve@mgh.harvard.edu, 28 Haz 2024 Cum, 16:25 tarihinde şunu yazdı:
You have an "extra large" defect that you will probably have to fix by hand. See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freev...
On 6/24/2024 12:42 PM, egemen gok wrote:
External Email - Use CautionThank you for your response. Okay, one more update. I tried recon-all for patients with T1. Unfortunately it doesnt work for my specific dataset. Neither functions like 5ttgen does not work from MRTrix.
I need to process this dataset for a huge study of our faculty. I hope we can fix this.
Kind regards Egemen
Douglas N. Greve dgreve@mgh.harvard.edu, 24 Haz 2024 Pzt, 16:48 tarihinde şunu yazdı:
Can you attach the log file. I can't read the pics you attached
On 6/18/2024 10:56 AM, egemen gok wrote:
External Email - Use Caution*Hello Freesurfer Developers*
recon-all is shutting down for some reason, this is the last lines of the code before shutting down. (It ran approximately 11-12 hours)
and fyi = I used flair image because there was no T1 image of the patient [image: image.png]
and this is the log file (recon-all.log) = [image: image.png]
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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%3E .
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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%3E .
You could try running SynthSR first, and then recon-all on the output of SynthSR. Cheers, /Eugenio
-- Juan Eugenio Iglesias http://www.jeiglesias.com
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of egemen gok egemen4552@gmail.com Date: Friday, June 28, 2024 at 22:31 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all is shutting down? because of flair?
External Email - Use Caution And btw the result of my recon-all is so terrible, I tried your method but it says lh.white is not loadable. In this situation, is it fixable when it has this much defect
[cid:ii_lxzi8oou3] egemen gok <egemen4552@gmail.commailto:egemen4552@gmail.com>, 29 Haz 2024 Cmt, 05:22 tarihinde şunu yazdı: My subjects have pathological tissues, is it fixable by your method? [cid:ii_lxzhya3d2]
Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu>, 28 Haz 2024 Cum, 16:25 tarihinde şunu yazdı: You have an "extra large" defect that you will probably have to fix by hand. See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freev... On 6/24/2024 12:42 PM, egemen gok wrote:
External Email - Use Caution Thank you for your response. Okay, one more update. I tried recon-all for patients with T1. Unfortunately it doesnt work for my specific dataset. Neither functions like 5ttgen does not work from MRTrix.
I need to process this dataset for a huge study of our faculty. I hope we can fix this.
Kind regards Egemen
Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu>, 24 Haz 2024 Pzt, 16:48 tarihinde şunu yazdı: Can you attach the log file. I can't read the pics you attached On 6/18/2024 10:56 AM, egemen gok wrote:
External Email - Use Caution Hello Freesurfer Developers
recon-all is shutting down for some reason, this is the last lines of the code before shutting down. (It ran approximately 11-12 hours)
and fyi = I used flair image because there was no T1 image of the patient [cid:ii_19061cc167fcb971f161]
and this is the log file (recon-all.log) = [cid:ii_19061cc167fcb971f162]
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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 .
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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 .
External Email - Use Caution
I'm not an expert in recon-all, but I wonder if recon-all has a sequence that distinguishes pathological tissue? I work primarily with MRtrix, and I need recon-all for the 5ttgen function from the MRtrix library. One of the features of 5ttgen is that it provides output segmented even for pathological tissue.
Honestly, I wasn't very satisfied with the results in terms of pathological tissue when I ran recon-all after synthSR and generated the 5ttgen output with recon-all. Instead of the tumor, it segmented the brainstem as pathologically.
In short, does recon-all have a feature to distinguish pathological tissue? If so, which sequence is it, and I will try to solve the problem by examining that sequence. If not, what would you recommend to me regarding this issue?
Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@mgh.harvard.edu, 29 Haz 2024 Cmt, 17:41 tarihinde şunu yazdı:
You could try running SynthSR first, and then recon-all on the output of SynthSR.
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
*From: *freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of egemen gok < egemen4552@gmail.com> *Date: *Friday, June 28, 2024 at 22:31 *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] recon-all is shutting down? because of flair?
External Email - Use Caution *And btw the result of my recon-all is so terrible, I tried your method but it says lh.white is not loadable. In this situation, is it fixable when it has this much defect
egemen gok egemen4552@gmail.com, 29 Haz 2024 Cmt, 05:22 tarihinde şunu yazdı:
My subjects have pathological tissues, is it fixable by your method?
Douglas N. Greve dgreve@mgh.harvard.edu, 28 Haz 2024 Cum, 16:25 tarihinde şunu yazdı:
You have an "extra large" defect that you will probably have to fix by hand. See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freev...
On 6/24/2024 12:42 PM, egemen gok wrote:
External Email - Use Caution *Thank you for your response. Okay, one more update. I tried recon-all for patients with T1.
Unfortunately it doesnt work for my specific dataset. Neither functions like 5ttgen does not work from MRTrix.
I need to process this dataset for a huge study of our faculty. I hope we can fix this.
Kind regards
Egemen
Douglas N. Greve dgreve@mgh.harvard.edu, 24 Haz 2024 Pzt, 16:48 tarihinde şunu yazdı:
Can you attach the log file. I can't read the pics you attached
On 6/18/2024 10:56 AM, egemen gok wrote:
External Email - Use Caution **Hello Freesurfer Developers*
recon-all is shutting down for some reason, this is the last lines of the code before shutting down. (It ran approximately 11-12 hours)
and fyi = I used flair image because there was no T1 image of the patient
and this is the log file (recon-all.log) =
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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%3E .
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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%3E .
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%3E .
No, it does not
On 6/29/2024 6:28 PM, egemen gok wrote:
External Email - Use Caution
I'm not an expert in recon-all, but I wonder if recon-all has a sequence that distinguishes pathological tissue? I work primarily with MRtrix, and I need recon-all for the 5ttgen function from the MRtrix library. One of the features of 5ttgen is that it provides output segmented even for pathological tissue.
Honestly, I wasn't very satisfied with the results in terms of pathological tissue when I ran recon-all after synthSR and generated the 5ttgen output with recon-all. Instead of the tumor, it segmented the brainstem as pathologically.
In short, does recon-all have a feature to distinguish pathological tissue? If so, which sequence is it, and I will try to solve the problem by examining that sequence. If not, what would you recommend to me regarding this issue?
Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@mgh.harvard.edu, 29 Haz 2024 Cmt, 17:41 tarihinde şunu yazdı:
You could try running SynthSR first, and then recon-all on the output of SynthSR. Cheers, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com *From: *freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of egemen gok <egemen4552@gmail.com> *Date: *Friday, June 28, 2024 at 22:31 *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> *Subject: *Re: [Freesurfer] recon-all is shutting down? because of flair? * External Email - Use Caution * And btw the result of my recon-all is so terrible, I tried your method but it says lh.white is not loadable. In this situation, is it fixable when it has this much defect egemen gok <egemen4552@gmail.com>, 29 Haz 2024 Cmt, 05:22 tarihinde şunu yazdı: My subjects have pathological tissues, is it fixable by your method? Douglas N. Greve <dgreve@mgh.harvard.edu>, 28 Haz 2024 Cum, 16:25 tarihinde şunu yazdı: You have an "extra large" defect that you will probably have to fix by hand. See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview On 6/24/2024 12:42 PM, egemen gok wrote: * External Email - Use Caution * Thank you for your response. Okay, one more update. I tried recon-all for patients with T1. Unfortunately it doesnt work for my specific dataset. Neither functions like 5ttgen does not work from MRTrix. I need to process this dataset for a huge study of our faculty. I hope we can fix this. Kind regards Egemen Douglas N. Greve <dgreve@mgh.harvard.edu>, 24 Haz 2024 Pzt, 16:48 tarihinde şunu yazdı: Can you attach the log file. I can't read the pics you attached On 6/18/2024 10:56 AM, egemen gok wrote: * External Email - Use Caution * *Hello Freesurfer Developers* recon-all is shutting down for some reason, this is the last lines of the code before shutting down. (It ran approximately 11-12 hours) and fyi = I used flair image because there was no T1 image of the patient and this is the log file (recon-all.log) = _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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> . _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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> . _______________________________________________ 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> .
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
egemen gok -
Iglesias Gonzalez, Juan E.