Re: [Freesurfer] [External] Freesurfer Digest, Vol 194, Issue 24

2020-04-20 Thread Douglas N. Greve 
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-requ...@nmr.mgh.harvard.edu 
 
> wrote:


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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" mailto:dgr...@mgh.harvard.edu>>
Subject: Re: [Freesurfer] cw256 option not working?
To: mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID: <92a8fb3b-7a8c-d31f-05c8-97983b590...@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
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End of Freesurfer Digest, Vol 194, Issue 24
***

Re: [Freesurfer] [External] Freesurfer Digest, Vol 194, Issue 24

2020-04-17 Thread Soichi Hayashi 
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-requ...@nmr.mgh.harvard.edu <
freesurfer-requ...@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
>
> 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-requ...@nmr.mgh.harvard.edu
>
> You can reach the person managing the list at
> freesurfer-ow...@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" 
> Subject: Re: [Freesurfer] cw256 option not working?
> To: 
> Message-ID: <92a8fb3b-7a8c-d31f-05c8-97983b590...@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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> End of Freesurfer Digest, Vol 194, Issue 24
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>
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