20 Apr
2020
20 Apr
'20
2:50 p.m.
Why are you including -hires? This should only be used if the voxel size is less than 1mm (yours is 1.05mm). There is no need to include either -hires or -cwd256
On 4/17/2020 6:08 PM, Soichi Hayashi wrote:
External Email - Use Caution
Douglas,
I've uploaded my t1. It should be named "soichi-cw256.nii.gz".
I am running the freesurfer with -debug option set now. I will reply back once I get the log.
Thank you! Soichi
On Fri, Apr 17, 2020 at 12:38 PM freesurfer-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu <freesurfer-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote:
This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources. ------- Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu <mailto:freesurfer-request@nmr.mgh.harvard.edu> You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu <mailto:freesurfer-owner@nmr.mgh.harvard.edu> When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: cw256 option not working? (Douglas N. Greve) ---------------------------------------------------------------------- Message: 1 Date: Fri, 17 Apr 2020 12:37:10 -0400 From: "Douglas N. Greve" <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> Subject: Re: [Freesurfer] cw256 option not working? To: <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <92a8fb3b-7a8c-d31f-05c8-97983b590217@mgh.harvard.edu <mailto:92a8fb3b-7a8c-d31f-05c8-97983b590217@mgh.harvard.edu>> Content-Type: text/plain; charset="utf-8" Can you run it with -debug as the first option and send me the (copious) terminal output? Even better if you can send me the data so I can try it out in the soon-to-be-released version 7. Instructions below From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log? into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu <http://surfer.nmr.mgh.harvard.edu> It will ask you for a user name: use "anonymous" (no quotes) It will ask you for a password: use "anonymous" (no quotes) cd transfer/incoming binary put subject.tar.gz Send an email that the file has been and the name of the file. On 4/17/2020 12:29 PM, Soichi Hayashi wrote: > > ????????External Email - Use Caution > > Hello. > > I am trying to run recon-all on HCP7T data and seeing this error message. > > **************************************** > ERROR! FOV=268.800 > 256 > Include the flag -cw256 with recon-all! > Inspect orig.mgz to ensure the head is fully visible. > **************************************** > > I've looked at orig.mgz, and it looks fine to me (screenshot attached). > > Anyway, I've added the -cw256 option to the command line. > > $ recon-all -i > ../5e977c0dfe00f4e4b4976207/5a052586eec2b300611abffc/t1.nii.gz > -subject output -all -parallel -openmp 8 -hippocampal-subfields-T1 > -hires -cw256 > > However, I am still seeing the same error message saying that I should > add the flag -cw256. Am I setting this option incorrectly? I am using > freesurfer version 6.0.0. > > Thank you! > Soichi Hayashi > Screenshot from 2020-04-17 12-28-01.png > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer