Re: [Freesurfer] Freesurfer Digest, Vol 199, Issue 7

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Hi Andrew

Thanks very much for this. I was able to patch the recon-all version in 7.1.0, not 7.1.1. When I tried it with 7.1.1 I received a "permission denied" to "mv recon-all recon-all.backup".

I then re-ran recon-all -autorecon1, -autorecon2, and -autorecon3 in 7.1.0. There was a Talairach error in autorecon1 and a few other errors in -autorecon2, and an "Unidentified variable" message at the end of -autorecon3.

When I run the $QA_TOOLS/recon_checker for this participant I get a long list of "ERROR .... missing output file" (and these output files are actually missing), as well as some commands and other outputs not found.

I"ve attached a zip file with the recon-all log.file, the recon_checker.log, a list of the errors I picked out of the recon-all.log, and the terminal output of the recon_checker that has a bit more info than the log file itself.

It seems there's still some significant problems--I hope you can guide me to a solution (e.g. perhaps remove 7.1.0 and reinstall 7.1.1?)

Cheers James

On Fri, Sep 11, 2020 at 7:04 PM Hoopes, Andrew AHOOPES@mgh.harvard.edu wrote:

Thanks for reporting this James. This is a bug in recon-all 7.1.1 that will be fixed in the next patch release. In the meantime, you can patch your version of recon-all with:

cd $FREESURFER_HOME/bin

mv recon-all recon-all.backup

curl https://raw.githubusercontent.com/freesurfer/freesurfer/fs-7.1/scripts/recon...

...

recon-all

chmod +x recon-all

Let me know if you still run into any issues.

Best

Andrew

*From: *James Hartzell james.hartzell@gmail.com *Date: *Friday, September 4, 2020 at 2:10 PM *To: *FS Help freesurfer@nmr.mgh.harvard.edu, "Hoopes, Andrew" < AHOOPES@mgh.harvard.edu> *Subject: *Re: Freesurfer Digest, Vol 199, Issue 7

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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:

1. Re: autorecon2, error MRISreadCurvature: (Hoopes, Andrew)
2. Re: recon-all error (Jie Zhao)
3. Re: mri_cvs_register with sub-millimeter recons (Zollei, Lilla,Ph.D.)
4. Re: recon-all error (Fischl, Bruce)
5. mri_segstats quetsion (Nasiriavanaki, Zahra)

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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:

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Hi

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.

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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