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?

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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:
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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:
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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) =
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