On Fri, Apr 17, 2020 at 12:38 PM freesurfer-request@nmr.mgh.harvard.edu <freesurfer-request@nmr.mgh.harvard.edu> wrote:

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Today's Topics:

1. Re: cw256 option not working? (Douglas N. Greve)

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Message: 1
Date: Fri, 17 Apr 2020 12:37:10 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] cw256 option not working?
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <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
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
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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