External Email - Use Caution 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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgr...@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: > 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 <cyfr...@hku.hk> wrote: >> >> >> 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 >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
