Hi Juhyoung

can you just cut and paste the text into the email instead of a screen shot?

thanks
Bruce
On Mon, 7 Aug 2017, Juhyoung Ryu wrote:

Sure, screenshot image is below with commands.

On Aug 7, 2017, at 11:14 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

can you send us the entire screeen output of that command?

On Mon, 7 Aug 2017, Juhyoung Ryu wrote:

Thank you for the response.

Then what do you suggest i use? Because same error is occurred when i typed like this; [recon-all -subject ${subjName} -i T1_bfc.nii -hires -T2 T2_bfc.nii -T2pial -all]

Thanks!
Juhyoung

On Aug 6, 2017, at 3:04 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

Hi Juhyoung

I think it's because you have -cw256. Since it comes after -hires it overrides it and tells recon-all to crop to a 256 volume size

cheers
Bruce
On Fri, 4 Aug 2017, Juhyoung Ryu wrote:

Dear FS experts,
I want to reconstruct white and pial surface using both -hires and -T2pial
options.
My T1 and T2 image resolution is .85mm^3.
But [recon-all -subject ${subjName} -i T1_bfc.nii -hires -T2 T2_bfc.nii -T2pial
-all -cw256] command is not working as I emailed below..
Is there any suggestions to run freesurfer?
Thank you in advance!
Juhyoung

    On Jul 28, 2017, at 8:45 AM, Juhyoung Ryu <jh67753737@gmail.com>
    wrote:
Hi Bruce,
Yes I’m using v6.0.
I found that there is -hires flag in version 6
(https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon)
and i included that;  recon-all -subject ${subjName} -i T1_bfc.nii -hires
-T2 T2_bfc.nii -T2pial -all -cw256
Thanks,
Juhyoung

    On Jul 28, 2017, at 2:19 AM, Bruce Fischl
    <fischl@nmr.mgh.harvard.edu> wrote:
Hi  Juhyoung
what FS version are you running with? If 6.0 you want to include
the -highres flag
cheers
Bruce
On Thu, 27 Jul 2017, juhyoung Ryu wrote:

    Hi experts,
    I'm trying to surface reconstruction using
    high-resolution T1 and T2 data
    using freesurfer version 6
    So I typed like this:
    recon-all -subject ${subjName} -i T1_bfc.nii -hires -T2
    T2_bfc.nii -T2pial
    -all
    and that excited with errors like this;
    \n****************************************
    ERROR! FOV=272.000 > 256
    Include the flag -cw256 with recon-all!
    Inspect orig.mgz to ensure the head is fully visible.
    ****************************************\n
    So I added -cw256 flag and run the command line again
    (recon-all -subject
    ${subjName} -i T1_bfc.nii -hires -T2 T2_bfc.nii -T2pial
    -all -cw256). But
    the result is same.
    I'd appreciate any suggestion.
    Thank you,
    Juhyoung
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