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 <jh67753...@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
      <fis...@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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