Hi FS team,

I encountered recon-all error and I want to solve the problem or find alternative method.
As you can see forwarded mail thread, I asked about the problem before but i couldn’t any clear answer..

Would you suggest someone to advice me how to deal with the problem?

Thanks,
Juhyoung

Begin forwarded message:

From: juhyoung Ryu <jh67753737@gmail.com>
Subject: Re: [Freesurfer] recon-all error: ERROR! FOV=272.000 > 256
Date: August 8, 2017 at 8:27:33 AM GMT+9
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>

===============================================================================================
server2:20170214_JEL JuhyoungRyu$ recon-all -subject JEL_v6 -i T1_bfc.nii -T2 T2_bfc.nii -T2pial -all -hires
INFO: hi-res volumes are conformed to the min voxel size
Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects
Actual FREESURFER_HOME /Applications/freesurfer
Darwin server2.local 16.6.0 Darwin Kernel Version 16.6.0: Fri Apr 14 16:21:16 PDT 2017; root:xnu-3789.60.24~6/RELEASE_X86_64 x86_64
/Applications/freesurfer/subjects/JEL_v6
\n mri_convert /Users/JuhyoungRyu/Desktop/subjects/20170214_JEL/T1_bfc.nii /Applications/freesurfer/subjects/JEL_v6/mri/orig/001.mgz \n
mri_convert.bin /Users/JuhyoungRyu/Desktop/subjects/20170214_JEL/T1_bfc.nii /Applications/freesurfer/subjects/JEL_v6/mri/orig/001.mgz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Users/JuhyoungRyu/Desktop/subjects/20170214_JEL/T1_bfc.nii...
TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.998342, 0, -0.057564)
j_ras = (0, 1, 0)
k_ras = (0.057564, 0, 0.998342)
writing to /Applications/freesurfer/subjects/JEL_v6/mri/orig/001.mgz...
#--------------------------------------------
#@# T2/FLAIR Input Mon Aug  7 11:54:55 KST 2017
/Applications/freesurfer/subjects/JEL_v6
\n mri_convert --no_scale 1 /Users/JuhyoungRyu/Desktop/subjects/20170214_JEL/T2_bfc.nii /Applications/freesurfer/subjects/JEL_v6/mri/orig/T2raw.mgz \n
mri_convert.bin --no_scale 1 /Users/JuhyoungRyu/Desktop/subjects/20170214_JEL/T2_bfc.nii /Applications/freesurfer/subjects/JEL_v6/mri/orig/T2raw.mgz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Users/JuhyoungRyu/Desktop/subjects/20170214_JEL/T2_bfc.nii...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.998342, 0, -0.057564)
j_ras = (0, 1, 0)
k_ras = (0.057564, 0, 0.998342)
writing to /Applications/freesurfer/subjects/JEL_v6/mri/orig/T2raw.mgz...
#--------------------------------------------
#@# MotionCor Mon Aug  7 11:55:00 KST 2017
Found 1 runs
/Applications/freesurfer/subjects/JEL_v6/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.
\n cp /Applications/freesurfer/subjects/JEL_v6/mri/orig/001.mgz /Applications/freesurfer/subjects/JEL_v6/mri/rawavg.mgz \n
/Applications/freesurfer/subjects/JEL_v6
\n mri_convert /Applications/freesurfer/subjects/JEL_v6/mri/rawavg.mgz /Applications/freesurfer/subjects/JEL_v6/mri/orig.mgz --conform_min \n
mri_convert.bin /Applications/freesurfer/subjects/JEL_v6/mri/rawavg.mgz /Applications/freesurfer/subjects/JEL_v6/mri/orig.mgz --conform_min 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Applications/freesurfer/subjects/JEL_v6/mri/rawavg.mgz...
TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.998342, 0, -0.057564)
j_ras = (0, 1, 0)
k_ras = (0.057564, 0, 0.998342)
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
Reslicing using trilinear interpolation 
writing to /Applications/freesurfer/subjects/JEL_v6/mri/orig.mgz...
\n****************************************
ERROR! FOV=272.000 > 256
Include the flag -cw256 with recon-all!
Inspect orig.mgz to ensure the head is fully visible.
****************************************\n
Darwin server2.local 16.6.0 Darwin Kernel Version 16.6.0: Fri Apr 14 16:21:16 PDT 2017; root:xnu-3789.60.24~6/RELEASE_X86_64 x86_64

recon-all -s JEL_v6 exited with ERRORS at Mon Aug  7 11:55:17 KST 2017

===============================================================================================

Here it is!

Thank you so much,
Juhyoung

On Mon, Aug 7, 2017 at 11:18 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
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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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.


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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.