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

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 <fis...@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 <fis...@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 <fis...@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 <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
>>>>>> _______________________________________________
>>>>>> Freesurfer mailing list
>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>> 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
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>>>>>> 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.
>>>>>>
>>>>> _______________________________________________
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>
>>>>>
>>>>> 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.
>>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> 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.
>>>
>>
>>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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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