Re: [Freesurfer] mrisComputeCorrelationTerm: delta is not finite at vno 0
I uploaded 3 set of T1.nii and T2.nii files for 3 example subjects.
You can get subject information here : T1_CUBEE{#subject}.nii
#0001 data success FS processing and #0002 / #0010 data is failed.
- Success: 0001
- Failed: 0010, 0002
I did FREESURFER processing using both T1 and T2 data after preprocessing and
downsampling from 0.85mm to 1mm resolution.
Thank you in advance for any help,
Juhyoung
> On Feb 6, 2017, at 11:39 PM, Bruce Fischl wrote:
>
> Hi Juhyoung
>
> can you upload one subject that this happens in to our ftp site?
>
> cheers
> Bruce
> On Mon, 6 Feb 2017, Juhyoung Ryu wrote:
>
>>
>> Hi FS developers,
>>
>> I received errors in one of steps in recon-all.
>> I analyzed 111 individual subjects' T1 data using same method, but there are
>> errors in only 14 subjects.
>>
>>
>>
>> Below is screenshot image in the end of recon-all.log file. I attached log
>> files from two exemplar subjects below, also.
>>
>> I’d appreciate if you might help me.
>> Juhyoung.
>>
>>
>>
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Re: [Freesurfer] mrisComputeCorrelationTerm: delta is not finite at vno 0
Hi Bruce,
Does 'entire subject directory tree' means that the subject’s data containing
all preprocessed results before i run FREESURFER? not only raw T1 and T2 file?
Thank you,
Juhyoung.
> On Feb 7, 2017, at 10:36 AM, Bruce Fischl wrote:
>
> Hi Juhyoung
>
> can you tar and gzip the entire subject directory tree and upload that?
>
> thanks
> Bruce
>
> On Tue, 7 Feb 2017, Juhyoung Ryu wrote:
>
>> I uploaded 3 set of T1.nii and T2.nii files for 3 example subjects.
>> You can get subject information here : T1_CUBEE{#subject}.nii
>>
>> #0001 data success FS processing and #0002 / #0010 data is failed.
>> - Success: 0001
>> - Failed: 0010, 0002
>>
>> I did FREESURFER processing using both T1 and T2 data after preprocessing
>> and downsampling from 0.85mm to 1mm resolution.
>>
>> Thank you in advance for any help,
>> Juhyoung
>>
>>> On Feb 6, 2017, at 11:39 PM, Bruce Fischl
>>> wrote:
>>>
>>> Hi Juhyoung
>>>
>>> can you upload one subject that this happens in to our ftp site?
>>>
>>> cheers
>>> Bruce
>>> On Mon, 6 Feb 2017, Juhyoung Ryu wrote:
>>>
>>>>
>>>> Hi FS developers,
>>>>
>>>> I received errors in one of steps in recon-all.
>>>> I analyzed 111 individual subjects' T1 data using same method, but there
>>>> are errors in only 14 subjects.
>>>>
>>>>
>>>>
>>>> Below is screenshot image in the end of recon-all.log file. I attached log
>>>> files from two exemplar subjects below, also.
>>>>
>>>> I’d appreciate if you might help me.
>>>> Juhyoung.
>>>>
>>>>
>>>>
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>>> properly
>>> dispose of the e-mail.
>>
>>
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>>
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Re: [Freesurfer] mrisComputeCorrelationTerm: delta is not finite at vno 0
Yes, I set FREESURFER_HOME variable as '/Applications/freesurfer’, which I installed freesurfer v6. I attached recon-all.log file below. I can see 'build-stamp.txt: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c’ in log file. Is there anything to check more? Thank you, Juhyoung recon-all.log Description: Binary data > On Feb 9, 2017, at 12:38 PM, Bruce Fischl wrote: > > sounds like you are using the old (5.2) recon-all. Are you sure it is 6 in > your path? > > And can you email the list so others can answer? > > thanks > Bruce > > > On Thu, 9 Feb 2017, Juhyoung Ryu wrote: > >> Hi Bruce, >> I installed FREESURFER with version 6.0 for your recommendation and I got an >> error: >> mri_em_register: could not open GCA >> /Applications/freesurfer/average/RB_all_2008-03-26.gca. >> That file not exist in ‘average' folder, and there is one similar >> file: RB_all_2016-05-10.vc700.gca >> Do you think I should drop that file manually from FREESURFER v5.2? >> Thank you in advance,Juhyoung >> >> Begin forwarded message: >> From: Juhyoung Ryu >> Subject: Re: [Freesurfer] mrisComputeCorrelationTerm: delta is not >> finite at vno 0 >> Date: February 8, 2017 at 11:01:23 AM GMT+9 >> To: Z K >> Cc: Bruce Fischl >> Hi Zeke and Bruce, >> Thank you very much for your help. >> I’ll try it now and share the results. >> Thanks! >> Juhyoung. >> >> On Feb 8, 2017, at 8:13 AM, Z K >> wrote: >> Hello Juhyoung, >> I noticed from the recon-all.log files that you are using >> freesurfer v5.2. It was revealed that this version had issues >> regarding systematic white surface contraction and placement of >> the pial surface extending too far: >> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-May/029581.html >> I would recommend processing these subjects with version 6.0 >> https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall >> -Zeke >> On 02/06/2017 01:43 AM, Juhyoung Ryu wrote: >> >> Hi FS developers, >> >> I received errors in one of steps in recon-all. >> I analyzed 111 individual subjects' T1 data using >> same method, but there >> are errors in _only 14 subjects._ >> >> Below is screenshot image in the end of >> recon-all.log file. I attached >> log files from two exemplar subjects below, also. >> >> I’d appreciate if you might help me. >> 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. ___ 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.
Re: [Freesurfer] mrisComputeCorrelationTerm: delta is not finite at vno 0
I checked version of recon-all script using 'recon-all -version’ command and 'freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c’ is printed. Juhyoung > On Feb 9, 2017, at 1:02 PM, Bruce Fischl wrote: > > What does > > which recon-all > > return? > >> On Feb 8, 2017, at 10:54 PM, Juhyoung Ryu wrote: >> >> Yes, I set FREESURFER_HOME variable as '/Applications/freesurfer’, which I >> installed freesurfer v6. >> I attached recon-all.log file below. >> I can see 'build-stamp.txt: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c’ >> in log file. >> >> Is there anything to check more? >> >> Thank you, >> Juhyoung >> >> >> >> >>> On Feb 9, 2017, at 12:38 PM, Bruce Fischl >>> wrote: >>> >>> sounds like you are using the old (5.2) recon-all. Are you sure it is 6 in >>> your path? >>> >>> And can you email the list so others can answer? >>> >>> thanks >>> Bruce >>> >>> >>>> On Thu, 9 Feb 2017, Juhyoung Ryu wrote: >>>> >>>> Hi Bruce, >>>> I installed FREESURFER with version 6.0 for your recommendation and I got >>>> an >>>> error: >>>> mri_em_register: could not open GCA >>>> /Applications/freesurfer/average/RB_all_2008-03-26.gca. >>>> That file not exist in ‘average' folder, and there is one similar >>>> file: RB_all_2016-05-10.vc700.gca >>>> Do you think I should drop that file manually from FREESURFER v5.2? >>>> Thank you in advance,Juhyoung >>>> >>>>Begin forwarded message: >>>> From: Juhyoung Ryu >>>> Subject: Re: [Freesurfer] mrisComputeCorrelationTerm: delta is not >>>> finite at vno 0 >>>> Date: February 8, 2017 at 11:01:23 AM GMT+9 >>>> To: Z K >>>> Cc: Bruce Fischl >>>> Hi Zeke and Bruce, >>>> Thank you very much for your help. >>>> I’ll try it now and share the results. >>>> Thanks! >>>> Juhyoung. >>>> >>>> On Feb 8, 2017, at 8:13 AM, Z K >>>> wrote: >>>> Hello Juhyoung, >>>> I noticed from the recon-all.log files that you are using >>>> freesurfer v5.2. It was revealed that this version had issues >>>> regarding systematic white surface contraction and placement of >>>> the pial surface extending too far: >>>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-May/029581.html >>>> I would recommend processing these subjects with version 6.0 >>>> https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall >>>> -Zeke >>>> On 02/06/2017 01:43 AM, Juhyoung Ryu wrote: >>>> >>>>Hi FS developers, >>>> >>>>I received errors in one of steps in recon-all. >>>>I analyzed 111 individual subjects' T1 data using >>>>same method, but there >>>>are errors in _only 14 subjects._ >>>> >>>>Below is screenshot image in the end of >>>>recon-all.log file. I attached >>>>log files from two exemplar subjects below, also. >>>> >>>>I’d appreciate if you might help me. >>>>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. >> > ___ 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.
Re: [Freesurfer] recon-all error in version 6: MRISread(lh.inflated): could not open file
Oh, sorry for that.
I pasted error message below;
#
#@# Curv .H and .K lh Mon Feb 13 20:27:14 KST 2017
/Applications/freesurfer/subjects/CUBEE0008/surf
\n mris_curvature -w lh.white.preaparc \n
total integrated curvature = 8.603*4pi (108.105) --> -8 handles
ICI = 179.6, FI = 2077.5, variation=31918.263
writing Gaussian curvature to
/Applications/freesurfer/subjects/CUBEE0008/surf/lh.white.preaparc.K...done.
writing mean curvature to
/Applications/freesurfer/subjects/CUBEE0008/surf/lh.white.preaparc.H...done.
rm -f lh.white.H
ln -s lh.white.preaparc.H lh.white.H
rm -f lh.white.K
ln -s lh.white.preaparc.K lh.white.K
\n mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated \n
normalizing curvature values.
averaging curvature patterns 5 times.
sampling 10 neighbors out to a distance of 10 mm
MRISread(lh.inflated): could not open file
thresholding curvature at 99.90% level
No such file or directory
mris_curvature: could not read surface file lh.inflated
No such file or directory
Actually I’m trying to run freesurfer using both T1 and T2 (0.85mm^3) and I
just took surface construction method in HCP (human connectome project)
pipeline like this;
recon-all -s "$subjID" -autorecon2 -nosmooth2 -noinflate2 -nocurvstats
-nosegstats
${CUBEEPIPEDIR}/FreeSurferHiresWhite.sh "$subjID" "$subjFSDIR" T1_bfc_gc.nii
T2_bfc_brain_gc.nii (Highres white stuff and Fine Tune T2w to T1w Reg)
recon-all -subjid "$subjID" -sd "$subjFSDIR" -smooth2 -inflate2 -curvstats
-sphere -surfreg -jacobian_white -avgcurv -cortparc
${CUBEEPIPEDIR}/FreeSurferHiresPial.sh $subjID $subjFSDIR T1_bfc_gc.nii
T2_bfc_brain_gc.nii (Highres pial stuff)
#Final Recon-all Steps
recon-all -subjid "$subjID" -sd "$subjFSDIR" -surfvolume -parcstats -cortparc2
-parcstats2 -cortparc3 -parcstats3 -cortribbon -segstats -aparc2aseg -wmparc
-balabels -label-exvivo-ec
I haven’t seen the error message such as 'mris_curvature: could not read
surface file lh.inflated’ when i use version 5.2.
I think this problem occurred as HCP team used freesurfer old version, then i’d
better mail to HCP team.
Thank you for all the supports again,
Juhyoung
> On Feb 14, 2017, at 12:39 AM, Bruce Fischl wrote:
>
> Hi Juhyoung
>
> First, can you please paste this kind of thing as text into your email
> instead of taking snapshots? That makes things easier for us.
>
> Second, why are you telling recon-all not to do the inflation with
> -noinflate2? That is why it can't find the inflated surface.
>
> cheers
> Bruce
>
>
> On Mon, 13 Feb 2017, Juhyoung Ryu wrote:
>
>> Hi freesurfer experts,
>> Thank you for all your help.
>>
>>
>> So, I’m re-running freesurfer using version 6, But I got one error message
>> after i type command like this: recon-all -s "$subjID" -autorecon2
>> -nosmooth2 -noinflate2 -nocurvstats -nosegstats
>>
>> And error message like this:
>>
>>
>> I’m trying to find this error using freesurfer_v6 in the mail archive, but I
>> couldn’t find the same thing.
>> Could you explain this error?
>>
>>
>> Thanks in advance for any help.
>> Juhyoung
>>
>>
>>> On Feb 10, 2017, at 4:54 AM, Douglas Merkitch
>>> wrote:
>>>
>>> The same thing happened to me on my mac when I changed the FREESURFER_HOME
>>> variable in the terminal, but not in the .bashrc file that I source when
>>> the terminal opens.
>>>
>>> Hope this helps!
>>>
>>> Thanks,
>>>
>>> Doug
>>>
>>> Douglas Merkitch
>>> Neurological Sciences
>>> Rush University Medical Center
>>>
>>>
>>>
>>> On Feb 9, 2017, at 1:49 PM, zkauf...@nmr.mgh.harvard.edu
>>> <mailto:zkauf...@nmr.mgh.harvard.edu> <mailto:zkauf...@nmr.mgh.harvard.edu
>>> <mailto:zkauf...@nmr.mgh.harvard.edu>> wrote:
>>>
>>>> Hello Juhyoung,
>>>>
>>>> If its complaining about "RB_all_2008-03-26.gca" then something must have
>>>> happened where you still have portions of the old freesurfer installed, or
>>>> your mixing versions because Freesurfer v6 has no mention of
>>>> RB_all_2008-03-26.gca. Please try completely removing the
>>>> /Applications/freesurfer directory and reinstalling v6.0.
>>>>
>>>> If this doesnt work please email me the exact command and error output.
>>>>
>>>>
>>>>
>>>>> Yes, I set FREESURFER_HOME variable as '/Applications/freesurfer', which I
>>&
[Freesurfer] recon-all error: ERROR! FOV=272.000 > 256
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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Re: [Freesurfer] recon-all error: ERROR! FOV=272.000 > 256
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 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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Re: [Freesurfer] recon-all error: ERROR! FOV=272.000 > 256
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
> <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 > <mailto: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
>> ___
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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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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
>> ${subjName} -i T1_bfc.nii -hires -T2 T2_bfc.nii -T2pial
>> -all -cw256). But
>> the result is same.
>> I'd appreciate any suggestion.
>> Thank you,
>> Juhyoung
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> The information in this e-mail is intended only for the person to
>> whom it is
>> addressed. If you believe this e-mail was sent to you in error and
>> the e-mail
>> contains patient information, please contact the Partners
>> Compliance HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to
>> you in error
>> but does not contain patient information, please contact the sender
>> and properly
>> dispose of the e-mail.
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
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Freesurfer mailing list
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Re: [Freesurfer] recon-all error: ERROR! FOV=272.000 > 256
===
server2:20170214_JEL JuhyoungRyu$ 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
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
>>> 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 ${subjName} -i T1_bfc.nii -hires -T2
>>>> T2_bfc.nii -T2pial -all]
>>>>
>>>> Thanks!
>>>> Juhyoung
>>>>
>>>> On Aug 6, 2017, at 3:04 AM, Bruce Fischl
>>>>> wrote:
>>>>>
>>>>> Hi Juhyoung
[Freesurfer] Fwd: recon-all error: ERROR! FOV=272.000 > 256
Hi FS team, I encountered recon-all error and I want to solve the problem or find alternative method. As you can see forwarded mail thread, I asked about the problem before but i couldn’t any clear answer.. Would you suggest someone to advice me how to deal with the problem? Thanks, Juhyoung > Begin forwarded message: > > From: juhyoung Ryu > Subject: Re: [Freesurfer] recon-all error: ERROR! FOV=272.000 > 256 > Date: August 8, 2017 at 8:27:33 AM GMT+9 > To: Freesurfer support list > > === > server2:20170214_JEL JuhyoungRyu$ 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 <mailto:fis...@nmr.mgh.harvard.edu>> wrote: > Hi Juhyoung > > can you just cut and paste the text into the email instead of a
Re: [Freesurfer] recon-all error: ERROR! FOV=272.000 > 256
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 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 && $FOV_gt_256) then > > > > and re-run with the hires flag. > > Alternatively, you can reduce the FOV to 256 or less with mri_convert --crop > and --crop-size. > > On 8/28/17 9:50 PM, Juhyoung Ryu wrote: >> Hi FS team, >> >> I encountered recon-all error and I want to solve the problem or find >> alternative method. >> As you can see forwarded mail thread, I asked about the problem before but i >> couldn’t any clear answer.. >> >> Would you suggest someone to advice me how to deal with the problem? >> >> Thanks, >> Juhyoung >> >>> Begin forwarded message: >>> >>> From: juhyoung Ryu mailto:jh67753...@gmail.com>> >>> Subject: Re: [Freesurfer] recon-all error: ERROR! FOV=272.000 > 256 >>> Date: August 8, 2017 at 8:27:33 AM GMT+9 >>> To: Freesurfer support list >> <mailto:freesurfer@nmr.mgh.harvard.edu>> >>> >>> === >>> server2:20170214_JEL JuhyoungRyu$ 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 /Applica
[Freesurfer] Resampling anatomical ROI to the functional images
External Email - Use Caution Hi all, I’d like to upsampling anatomical ROI data, what i created using ribbon file, to the functional resolution. As the anatomical and functional data were aligned, I need only re-slice processing except for coregistration. I tried upsampling using ‘mir_label2vol’, but i have no idea to create ‘register.dat’ file. ‘mri_convert’ with —voxsize flag provides upsampling, but that was all. Would you help me to re-slice ROI data to the functional coordinate? Thank you in advance, Juhyoung ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Resampling anatomical ROI to the functional images
External Email - Use Caution Hi Douglas, Thank you for the response. I tried to figure out your suggestion, but as i understand about bbregister, it provides registration of functional space to anatomical space in $subjects_dir. As what i want to do is registration of anatomical data to functional space by upsampling process, I have no idea how to use the command. Additionally, I don’t want alignment between anatomical and functional data. Could you please tell me more about your suggestion? Thank you very much in advance! Juhyoung > On 15 Apr 2019, at 11:42 PM, Greve, Douglas N.,Ph.D. > wrote: > > Use bbregister to create the register.dat file. Run it with --help to > get docs on how to use it. > > On 4/15/2019 7:51 AM, Juhyoung Ryu wrote: >> External Email - Use Caution >> >> Hi all, >> >> I’d like to upsampling anatomical ROI data, what i created using ribbon >> file, to the functional resolution. >> As the anatomical and functional data were aligned, I need only re-slice >> processing except for coregistration. >> >> I tried upsampling using ‘mir_label2vol’, but i have no idea to create >> ‘register.dat’ file. >> ‘mri_convert’ with —voxsize flag provides upsampling, but that was all. >> >> Would you help me to re-slice ROI data to the functional coordinate? >> >> >> Thank you in advance, >> Juhyoung >> >> ___ >> 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
