Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

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Hi Bruce,

I uploaded the recon-all.log file and the zip file of the entire subject dir to my dropbox. Please download them through the following shared link:

Recon-all.log file: https://www.dropbox.com/s/sona1xycmdr7jma/Terminal%20Saved%20Output%3B%20exi...

Zip file of the entire subject dir: https://www.dropbox.com/s/r1uvd2ngyap7klp/subject%20dir%20%28exited%20with%2...

Please take your time. Thank you very much.

Regards

Frank

________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: 12 March 2020 22:07 To: Freesurfer support list Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

Hi Frank

sorry, I've been busy with local deadlines that are over now. Can you send us the recon-all.log file? Or tar and gzip the entire subject dir and upload it to our ftp site? Apologies if any of this has been done.

cheers Bruce

On Thu, 12 Mar 2020, Frank Chau wrote:

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Dear Douglas ,

How could I find out the root cause of this recon-all "exited with ERRORS"? Does it mean there are flaws in the generated output? Or I could ignore this error warning? Thank you.

Regards

Frank ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: 11 March 2020 21:52 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

it should not really affect it

On 3/10/2020 10:22 AM, Tim Schäfer wrote:

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Maybe Doug or Bruce should comment on that, but afaik that should not affect your analysis at all: recon-all will resample your data to 256x256x256 (as part of creating what FreeSurfer calls the 'conformed' version of the image) anyways.

The error you get, if I understand correctly from the logs, is that *after* the resampling, the FOV *still* is not 256.

Best,

Tim

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On March 9, 2020 at 7:34 PM Frank Chau cyfrank@hku.hk wrote:

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Dear Tim,

The FOV of my T1 series is 256 x 240. Is it the FOV of the T1 series will affect the process Recon-all? If yes, how would it impact my output results?

Regards

Frank ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Frank Chau cyfrank@hku.hk Sent: 06 March 2020 22:17 To: Freesurfer support list Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

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Dear Tim,

The FOV of my T1 series is 256 x 240. Is it the FOV of the T1 series will affect the process Recon-all? If yes, how would it impact my output results?

Regards

Frank

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From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Tim Schäfer ts+ml@rcmd.org Sent: 05 March 2020 2:25 To: Freesurfer support list Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

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Thanks for providing the image. Looks fine to me as well.

What is a bit strange is that when running `mri_info` on the file you provided, it shows a FOV of 256 (not 284!) for me, so I have no idea why this error is triggered in recon-all.

Maybe somebody else has an idea...

Tim

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On March 4, 2020 at 4:47 PM Frank Chau cyfrank@hku.hk wrote:

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Dear Tim,

I have checked the orig.mgz file and nothing usual was found (please see the attachment image)

For downloading my orig.mgz: https://www.dropbox.com/s/crkndenx8ev957v/orig.mgz?dl=0

Regards

Frank

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From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Tim Schäfer ts+ml@rcmd.org Sent: 04 March 2020 23:27 To: Freesurfer support list Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

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Dear Frank,

if you search the log in your Dropbox for 'error', this comes up:

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ERROR! FOV=284.000 > 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible.

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Did you have a look at the orig.mgz?

Best,

Tim

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On March 4, 2020 at 2:59 PM Frank Chau cyfrank@hku.hk wrote:

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Hello FreeSurfer Developers,

I ran a recon-all on a recent batch of T1 Nifti files and all ended with "exited with ERRORS". For example: "recon-all -s Chan_Pui_Kim_42M_T1 exited with ERRORS at Sat Jan 11 01:32:55 HKT 2020".

I've searched the email archive list and I found other researcher encountered same problem before. However, I am quite sure their root causes are not same as my case. 3 possible causes were found in the email archive which about "exited with ERRORS":

1. The version of freesurfer (I have already used the latest 6.0.0 version)
2. Hard disk space (My computer have enough hard disk space)
3. sharing folder between virtual machine and original platform. (I use freesurfer in Mac OS which do not have this problem)

I uploaded the recon-all.log to my dropbox in case it's of any use.

1. FreeSurfer version: Darwin-OSX-stable-pub-v6.0.0-2beb96c

2. Platform: MAC OS X 10.11.6

3. uname -a: Darwin PFCs-MacBook-Pro.local 15.6.0 Darwin Kernel Version 15.6.0: Thu Jun 21 20:07:40 PDT 2018; root:xnu-3248.73.11~1/RELEASE_X86_64 x86_64

4. recon-all.log, please download at:

https://www.dropbox.com/s/bxb2vyhz3koo83s/recon-all.log-%20Terminal%20Output...

Regards

Frank

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FRANK C Y CHAU

Research assistant

Division of Neurology

Department of Medicine

Tel: +852 6340 2553

Fax: 2872 5828

E-mail : cyfrank@hku.hkmailto:cyfrank@hku.hk

Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong

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