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> .