Hi Laurel

if a subject dir already exists recon-all will exit unless you specify -force. Alternatively you can try using the -make all flag, which should rerun only the steps that are needed (assuming the reboot didn't happen e.g. in the middle of writing a file)

cheers Bruce On Tue, 28 Jan 2020, Laurel Quinlan wrote:

External Email - Use Caution

Hi Doug,

Thanks for looking over that file. It is the correct recon-all file for one of the problem brains. I discovered that there was a system reboot of some sort when the recon-all was processing for these problem brains, so that is likely what caused the process to stop. How can I restart the recon-all process for these brains? I have tried just rerunning the recon-all command but the process exits within a few moments each time. I am wondering if there is something I need to delete that was partially processed during the first attempt.

Thanks,

Laurel

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From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Friday, January 24, 2020 9:34 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all errors - mri_segstats and mri_relabel_hypointensities   It did not look like there was an explicit error in that log file, it just stops at mris_volmask. Is that the right recon-all? Also, please just send the text file so that we don't have to unzip it.

On 1/22/2020 4:39 PM, Laurel Quinlan wrote:

          External Email - Use Caution        

Hi FS Support,

I have two brains for which recon-all exited with errors after I edited the wm.mgz volume. It seems that the problem occurs during the mri_segstats and mri_relabel_hypointensities steps (if I'm reading the output of the command "tail scripts/recon-all.log" correctly). I attached one of the recon-all.log files as a zipped txt file. Please let me know if you have troubleshooting suggestions.

Thank you for your help!

Laurel Quinlan Research Specialist Center for Healthy Minds University of Wisconsin-Madison

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

glad to hear it Bruce On Fri, 31 Jan 2020, Laurel Quinlan wrote:

External Email - Use Caution

Hi Bruce,

Thank you for your help! I removed the IsRunning.lh+rh script as well and reran the recon. Everything seems to have worked!

-Laurel

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From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Tuesday, January 28, 2020 3:37 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Cc: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Subject: Re: [Freesurfer] recon-all errors - mri_segstats and mri_relabel_hypointensities   Hi Laurel

if a subject dir already exists recon-all will exit unless you specify -force. Alternatively you can try using the -make all flag, which should rerun only the steps that are needed (assuming the reboot didn't happen e.g. in the middle of writing a file)

cheers Bruce On Tue, 28 Jan 2020, Laurel Quinlan wrote:

...

External Email - Use Caution

Hi Doug,

Thanks for looking over that file. It is the correct recon-all file for

one

...

of the problem brains. I discovered that there was a system reboot of some sort when the recon-all was processing for these problem brains, so that

is

...

likely what caused the process to stop. How can I restart the recon-all process for these brains? I have tried just rerunning the recon-all

command

...

but the process exits within a few moments each time. I am wondering if there is something I need to delete that was partially processed during

the

...

first attempt.

Thanks,

Laurel

---

_

...

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Friday, January 24, 2020 9:34 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all errors - mri_segstats and mri_relabel_hypointensities   It did not look like there was an explicit error in that log file, it just stops at mris_volmask. Is that the right recon-all? Also, please just send the text file so that we don't have to unzip it.

On 1/22/2020 4:39 PM, Laurel Quinlan wrote:

External Email - Use Caution

Hi FS Support,

I have two brains for which recon-all exited with errors after I edited the wm.mgz volume. It seems that the problem occurs during the mri_segstats and mri_relabel_hypointensities steps (if I'm reading the output of the command "tail scripts/recon-all.log" correctly). I attached one of the recon-all.log files as a zipped txt file. Please let me know if you have troubleshooting suggestions.

Thank you for your help!

Laurel Quinlan Research Specialist Center for Healthy Minds University of Wisconsin-Madison

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer