Re: [Freesurfer] recon-all error: ERROR! FOV=272.000 > 256
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 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
>> 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
>> 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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>> whom it is
>> addressed. If you believe this e-mail was sent to you in error and
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>> Compliance HelpLine at
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Re: [Freesurfer] recon-all error: ERROR! FOV=272.000 > 256
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 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
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
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 e-mail
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[Freesurfer] Thalamus ROI
Hi Freesurfer team, Is it possible to extract Thalamus as an ROI from aseg.mgz to be used for tractography in FSL. If so, what command I have to use to extract it. Can I use the LUT table to extract thalamus? Thanks, Sara ___ 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] TRACULA ERROR!!
Dear fellow researchers, I am running tracula pre-processing step, and the computer showed an error message: Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz Brain mask for output subject: Segmentation fault (core dumped) Linux Brain 4.2.0-27-generic #32~14.04.1-Ubuntu SMP Fri Jan 22 15:32:26 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Sun Aug 6 23:37:59 EDT 2017 I am sure that I have the aparc+aseg file in the right directory but it showed that the files are missing. I would be really appreciated if anyone could please help!!! Thanks so much!!! PS: I attached trac-all.log as an attachment. Thanks Sincerely, Ariel Sun Aug 6 18:19:37 EDT 2017 /media/brain/brains/TN_retro/Tracula /usr/local/freesurfer/bin/trac-all -prep -c dmrirc Subject AN01 SUBJECTS_DIR /media/brain/brains/TN_retro/Tracula FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c root Brain Linux Brain 4.2.0-27-generic #32~14.04.1-Ubuntu SMP Fri Jan 22 15:32:26 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize8192 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 15430 maxlocks unlimited maxsignal15430 maxmessage 819200 maxnice 0 maxrtprio0 maxrttimeunlimited total used free sharedbuffers cached Mem: 39716123064872 906740 53912 6797921089976 -/+ buffers/cache:12951042676508 Swap: 4117500 158044101696 Program versions: $Id: trac-all,v 1.60.2.1 2016/12/20 17:04:05 zkaufman Exp $ mri_convert.bin --all-info ProgramName: mri_convert.bin ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/06-22:19:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: root Machine: Brain Platform: Linux PlatformVersion: 4.2.0-27-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $ $Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $ ProgramName: dmri_motion ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/06-22:19:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: root Machine: Brain Platform: Linux PlatformVersion: 4.2.0-27-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/06-22:19:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: root Machine: Brain Platform: Linux PlatformVersion: 4.2.0-27-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/06-22:19:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: root Machine: Brain Platform: Linux PlatformVersion: 4.2.0-27-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/06-22:19:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: root Machine: Brain Platform: Linux PlatformVersion: 4.2.0-27-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/06-22:19:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: root Machine: Brain Platform: Linux PlatformVersion: 4.2.0-27-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_group ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/06-22:19:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: root Machine: Brain Platform: Linux PlatformVersion: 4.2.0-27-generic CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc root Brain Linux Brain 4.2.0-27-generic #32~14.04.1-Ubuntu SMP Fri Jan 22 15:32:26 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize8192 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 15430 maxlocks unlimited maxsignal15430 maxmessage 819200 maxnice 0 maxrtprio0 maxrttimeunlimited total used free sharedbuffers cached Mem: 39716123068316 903296 53912 6798561092544 -/+ buffers/cache:12959162675696 Swap: 4117500 158044101696 #- /usr/local/freesurfer/bin/trac-preproc #- #@# Image corrections Sun
