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 "$subjFSDIR" -surfvolume -parcstats -cortparc2 -parcstats2 -cortparc3 -parcstats3 -cortribbon -segstats -aparc2aseg -wmparc -balabels -label-exvivo-ec
I haven’t seen the error message such as 'mris_curvature: could not read surface file lh.inflated’ when i use version 5.2. I think this problem occurred as HCP team used freesurfer old version, then i’d better mail to HCP team.
Thank you for all the supports again, Juhyoung
On Feb 14, 2017, at 12:39 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Juhyoung
First, can you please paste this kind of thing as text into your email instead of taking snapshots? That makes things easier for us.
Second, why are you telling recon-all not to do the inflation with -noinflate2? That is why it can't find the inflated surface.
cheers Bruce
On Mon, 13 Feb 2017, Juhyoung Ryu wrote:
Hi freesurfer experts, Thank you for all your help.
So, I’m re-running freesurfer using version 6, But I got one error message after i type command like this: recon-all -s "$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 Douglas_Merkitch@rush.edu 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, zkaufman@nmr.mgh.harvard.edu mailto:zkaufman@nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu mailto:zkaufman@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 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 <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>> 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 <jh67753737@gmail.com mailto:jh67753737@gmail.com <mailto:jh67753737@gmail.com mailto:jh67753737@gmail.com>> > 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 <zkaufman@nmr.mgh.harvard.edu mailto:zkaufman@nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu mailto:zkaufman@nmr.mgh.harvard.edu>> > Cc: Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>> > 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 > <zkaufman@nmr.mgh.harvard.edu mailto:zkaufman@nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu mailto:zkaufman@nmr.mgh.harvard.edu>> 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://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed... https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_pipermail__freesurfer_2013-2DMay_029581.html&d=DwIFAw&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=tbfGn9PX8Y7JNwBmOKbl0cqEDAJdta1JKDch4R2RH-Q&s=a958-NuaRasmvxPlNYQGH7Xxuni1ja2_K-IPFKTdb38&e= <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed... https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_pipermail__freesurfer_2013-2DMay_029581.html&d=DwIFAw&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=tbfGn9PX8Y7JNwBmOKbl0cqEDAJdta1JKDch4R2RH-Q&s=a958-NuaRasmvxPlNYQGH7Xxuni1ja2_K-IPFKTdb38&e=> > I would recommend processing these subjects with version 6.0 > https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.... https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_DownloadAndInstall&d=DwIFAw&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=tbfGn9PX8Y7JNwBmOKbl0cqEDAJdta1JKDch4R2RH-Q&s=IZpj2AG9on5kqVAJyeidyZ75SJP8XLstoGw15-oiJMk&e= <https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.... https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_DownloadAndInstall&d=DwIFAw&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=tbfGn9PX8Y7JNwBmOKbl0cqEDAJdta1JKDch4R2RH-Q&s=IZpj2AG9on5kqVAJyeidyZ75SJP8XLstoGw15-oiJMk&e=> > -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. 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