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
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
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 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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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 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 mailto: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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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.
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
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.
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
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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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.
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
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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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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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
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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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.
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 ${subjName} -i T1_bfc.nii -hires -T2 T2_bfc.nii -T2pial -all -cw256). But the result is same. I'd appreciate any suggestion. Thank you, Juhyoung
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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=================== ============================================================================
server2:20170214_JEL JuhyoungRyu$ 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 ${subjName} -i T1_bfc.nii -hires -T2 T2_bfc.nii -T2pial -all -cw256). But the result is same. I'd appreciate any suggestion. Thank you, Juhyoung
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Hi FS team,
I encountered recon-all error and I want to solve the problem or find alternative method. As you can see forwarded mail thread, I asked about the problem before but i couldn’t any clear answer..
Would you suggest someone to advice me how to deal with the problem?
Thanks, Juhyoung
Begin forwarded message:
From: juhyoung Ryu jh67753737@gmail.com Subject: Re: [Freesurfer] recon-all error: ERROR! FOV=272.000 > 256 Date: August 8, 2017 at 8:27:33 AM GMT+9 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
=============================================================================================== server2:20170214_JEL JuhyoungRyu$ 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 mailto: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 mailto: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 mailto: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 <mailto: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 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 <mailto: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 ${subjName} -i T1_bfc.nii -hires -T2 T2_bfc.nii -T2pial -all -cw256). But the result is same. I'd appreciate any suggestion. Thank you, Juhyoung
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Currently recon-all requires that the FOV be 256 or less. This was an oversight on our part as I think it should work if it is > 256. Can you experiment for us? The easy thing to do is to simply disable the check for this. To do this, create a version of recon-all that you can edit. Find the line that says:
if ($FOV_gt_256) then
and change it to
if (0 && $FOV_gt_256) then
and re-run with the hires flag.
Alternatively, you can reduce the FOV to 256 or less with mri_convert --crop and --crop-size.
On 8/28/17 9:50 PM, Juhyoung Ryu wrote:
Hi FS team,
I encountered recon-all error and I want to solve the problem or find alternative method. As you can see forwarded mail thread, I asked about the problem before but i couldn’t any clear answer..
Would you suggest someone to advice me how to deal with the problem?
Thanks, Juhyoung
Begin forwarded message:
*From: *juhyoung Ryu <jh67753737@gmail.com mailto:jh67753737@gmail.com> *Subject: **Re: [Freesurfer] recon-all error: ERROR! FOV=272.000 > 256* *Date: *August 8, 2017 at 8:27:33 AM GMT+9 *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>
=============================================================================================== server2:20170214_JEL JuhyoungRyu$ 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 mailto: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 <mailto: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 <mailto: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 <mailto: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 <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 <mailto: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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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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Thanks Greve!
Command with ‘-hires’ and ‘-hires -cw256’ flag both work without any error message.
Thank you again!! Juhyoung
On Sep 4, 2017, at 7:36 AM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Currently recon-all requires that the FOV be 256 or less. This was an oversight on our part as I think it should work if it is > 256. Can you experiment for us? The easy thing to do is to simply disable the check for this. To do this, create a version of recon-all that you can edit. Find the line that says: if ($FOV_gt_256) then and change it to
if (0 && $FOV_gt_256) then
and re-run with the hires flag.
Alternatively, you can reduce the FOV to 256 or less with mri_convert --crop and --crop-size.
On 8/28/17 9:50 PM, Juhyoung Ryu wrote:
Hi FS team,
I encountered recon-all error and I want to solve the problem or find alternative method. As you can see forwarded mail thread, I asked about the problem before but i couldn’t any clear answer..
Would you suggest someone to advice me how to deal with the problem?
Thanks, Juhyoung
Begin forwarded message:
From: juhyoung Ryu <jh67753737@gmail.com mailto:jh67753737@gmail.com> Subject: Re: [Freesurfer] recon-all error: ERROR! FOV=272.000 > 256 Date: August 8, 2017 at 8:27:33 AM GMT+9 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>
=============================================================================================== server2:20170214_JEL JuhyoungRyu$ 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 mailto: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 mailto: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 mailto: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 <mailto: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 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 <mailto: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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Juhyoung Ryu