External Email - Use Caution
HI Andrew
Thanks. I've run autorecon 1, 2, and 3 so far for this one participant. There's an error in autorecon 1 but I see from older list discussion that it can be safely ignored. Even though autorecon 2 claims to finish without error, the error I reported seemed likely significant and I thought probably it should not be ignored--perhaps I am mistaken. I've attached a zip file with all the logs in the scripts folder.
Cheers James
On Fri, Sep 4, 2020 at 6:01 PM freesurfer-request@nmr.mgh.harvard.edu wrote:
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Today's Topics:
- Re: autorecon2, error MRISreadCurvature: (Hoopes, Andrew)
- Re: recon-all error (Jie Zhao)
- Re: mri_cvs_register with sub-millimeter recons (Zollei, Lilla,Ph.D.)
- Re: recon-all error (Fischl, Bruce)
- mri_segstats quetsion (Nasiriavanaki, Zahra)
Message: 1 Date: Thu, 3 Sep 2020 20:18:22 +0000 From: "Hoopes, Andrew" AHOOPES@mgh.harvard.edu Subject: Re: [Freesurfer] autorecon2, error MRISreadCurvature: To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: 67B3E641-B123-4261-880B-BF3E194A8B87@mgh.harvard.edu Content-Type: text/plain; charset="utf-8"
Hi James,
Can you send the full recon-all.log for this subject?
Thanks, Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of James Hartzell james.hartzell@gmail.com Reply-To: FS Help freesurfer@nmr.mgh.harvard.edu Date: Thursday, September 3, 2020 at 10:20 AM To: FS Help freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] autorecon2, error MRISreadCurvature:
External Email - Use CautionHi
When running recon-all autorecon2, on a single subject with (Macbook Pro 10.15.6 (19G2021), freesurfer-darwin-macOS-7.1.0-20200511-813297b)
it handles the rh.curv without a problem, but for the lh kicks out this error:
/Users...$subj.../surf \n mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm $subj lh curv sulc \n Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ $subj./lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture...error: No such file or directory error: MRISreadCurvature: could not open /Users/$subj./surf/lh.curv
***WARNING!*** Some error has occurred while reading 'lh.curv'. This might be due a vertex incompatibility between the surface 'lh.smoothwm' and curv 'lh.curv'.
You might be able to correct this by re-running 'mris_make_surfaces' on this dataset.
Skipping this (and any remaining) curvature files. Any measurements / calcuations that depend on the curvature file will be skipped.
Note /Users/$subj./surf/lh.curv does exist in the subject's surf folder.
I ran it twice just to be sure. I don't find an answer for the problem in the freesurfer list. Any guidance will be much appreciated! Cheers James Hartzell, PhD (2x) Donostia-San Sebati?n, Spain