External Email - Use Caution
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
On March 9, 2020 at 7:34 PM Frank Chau cyfrank@hku.hk wrote:
External Email - Use CautionDear 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"
External Email - Use CautionDear 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 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"
External Email - Use CautionThanks 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 cyfrank@hku.hk wrote:
External Email - Use CautionDear 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-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"
External Email - Use CautionDear 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 cyfrank@hku.hk wrote:
External Email - Use CautionHello 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":
- The version of freesurfer (I have already used the latest 6.0.0 version)
- Hard disk space (My computer have enough hard disk space)
- 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.
FreeSurfer version: Darwin-OSX-stable-pub-v6.0.0-2beb96c
Platform: MAC OS X 10.11.6
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
recon-all.log, please download at:
https://www.dropbox.com/s/bxb2vyhz3koo83s/recon-all.log-%20Terminal%20Output...
Regards
Frank
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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