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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