External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Frank Chau
<cyfr...@hku.hk>
Sent: 06 March 2020 22:17
To: Freesurfer support list
Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Tim Schäfer
<ts...@rcmd.org>
Sent: 05 March 2020 2:25
To: Freesurfer support list
Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"
External Email - Use Caution
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
> On March 4, 2020 at 4:47 PM Frank Chau <cyfr...@hku.hk> wrote:
>
>
> External Email - Use Caution
>
> 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
>
> ________________________________________
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Tim Schäfer
> <ts...@rcmd.org>
> Sent: 04 March 2020 23:27
> To: Freesurfer support list
> Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"
>
> External Email - Use Caution
>
> Dear Frank,
>
> if you search the log in your Dropbox for 'error', this comes up:
>
> ----
> ERROR! FOV=284.000 > 256
> Include the flag -cw256 with recon-all!
> Inspect orig.mgz to ensure the head is fully visible.
> ----
>
> Did you have a look at the orig.mgz?
>
> Best,
>
> Tim
>
>
> > On March 4, 2020 at 2:59 PM Frank Chau <cyfr...@hku.hk> wrote:
> >
> >
> > External Email - Use Caution
> >
> > 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%20log%2020%20Jan%202020%20.txt?dl=0
> >
> >
> >
> > Regards
> >
> > Frank
> >
> > ---------------------------
> >
> > FRANK C Y CHAU
> >
> >
> >
> > Research assistant
> >
> > Division of Neurology
> >
> > Department of Medicine
> >
> >
> >
> > Tel: +852 6340 2553
> >
> > Fax: 2872 5828
> >
> >
> >
> > E-mail : cyfr...@hku.hk<mailto:cyfr...@hku.hk>
> >
> >
> >
> >
> >
> > Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam Road,
> > Hong Kong
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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