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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