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]
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