7 Feb
2019
7 Feb
'19
5:38 p.m.
The problem is that matlab is calling the mris_fwhm though a forked shell. When this shell starts up, it does not have the right environment. This is not easy for me to troubleshoot remotely. Do you have a linux system adminstrator who can help you?
On 1/30/19 10:26 AM, Amrita Bedi wrote:
External Email - Use Caution
Good Morning Dr Greve,
Here is what I got:
system('mris_fwhm')
mris_fwhm: /home/apps/matlab/MATLAB/R2011b/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_fwhm)
ans =
1
Do you think this error has to do with the version of matlab I am using perhaps?
Best Amrita
On Tuesday, January 29, 2019, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
That looks ok. It must be something happening when you start a shell from matlab. What happens if you start matlab, then type system('mris_fwhm') On 1/29/19 9:39 AM, Amrita Bedi wrote: > > External Email - Use Caution > > Hi Drs Greve and Fischl, > > I tried the mris_fwhm command and got the following. Not sure if this > is helpful or not. > > bash-4.2$ mris_fwhm > USAGE: mris_fwhm > Smooths surface data and/or estimates FWHM > --i input > --subject subject (--s) > --hemi hemi (--h), or --lh or --rh > --surf surf <white> > --label labelfile > --cortex : used hemi.cortex.label > --mask maskfile > --X x.mat : matlab4 detrending matrix > --detrend order : polynomial detrending (default 0, turned off with > output) > --smooth-only : only smooth (implies --no-detrend) > --no-detrend : turn of poly detrending > --sqr : compute square of input before smoothing > --sum sumfile > --dat datfile (only contains fwhm) > --ar1dat ar1datfile (contains ar1mean ar1std) > --ar1 ar1vol : save spatial ar1 as an overlay > --prune - remove any voxel that is zero in any subject (after any > inversion) > --no-prune - do not prune (default) > --out-mask outmask : save final mask > > --fwhm fwhm : apply before measuring > --niters-only <niters> : only report on niters for fwhm > --o output > > --sd SUBJECTS_DIR > --synth > --synth-frames nframes : default is 10 > --threads nthreads > > --debug turn on debugging > --checkopts don't run anything, just check options and exit > --help print out information on how to use this program > --version print out version and exit > > $Id: mris_fwhm.c,v 1.40.2.4 2016/12/08 22:02:40 zkaufman Exp $ > > > > Best > Amrita > ---------- Forwarded message ---------- > From: *Amrita Bedi* <amibedi273@gmail.com <mailto:amibedi273@gmail.com> <mailto:amibedi273@gmail.com <mailto:amibedi273@gmail.com>>> > Date: Friday, January 25, 2019 > Subject: Functional connectivty walkthrough step 8 error > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > Ok hopefully, the text is visible now. > > bash-4.2$ mris_fwhm > USAGE: mris_fwhm > Smooths surface data and/or estimates FWHM > --i input > --subject subject (--s) > --hemi hemi (--h), or --lh or --rh > --surf surf <white> > --label labelfile > --cortex : used hemi.cortex.label > --mask maskfile > --X x.mat : matlab4 detrending matrix > --detrend order : polynomial detrending (default 0, turned off with > output) > --smooth-only : only smooth (implies --no-detrend) > --no-detrend : turn of poly detrending > --sqr : compute square of input before smoothing > --sum sumfile > --dat datfile (only contains fwhm) > --ar1dat ar1datfile (contains ar1mean ar1std) > --ar1 ar1vol : save spatial ar1 as an overlay > --prune - remove any voxel that is zero in any subject (after any > inversion) > --no-prune - do not prune (default) > --out-mask outmask : save final mask > > --fwhm fwhm : apply before measuring > --niters-only <niters> : only report on niters for fwhm > --o output > > --sd SUBJECTS_DIR > --synth > --synth-frames nframes : default is 10 > --threads nthreads > > --debug turn on debugging > --checkopts don't run anything, just check options and exit > --help print out information on how to use this program > --version print out version and exit > > $Id: mris_fwhm.c,v 1.40.2.4 2016/12/08 22:02:40 zkaufman Exp $ > > > > On Friday, January 25, 2019, Amrita Bedi <amibedi273@gmail.com <mailto:amibedi273@gmail.com> > <mailto:amibedi273@gmail.com <mailto:amibedi273@gmail.com>>> wrote: > > Sorry for the confusion. The Va doesn’t let us access our gmails > so I’ll send an email with the text from my city mail email address. > > On Friday, January 25, 2019, 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: > > Hi Amrita > > please don't take an image of the text and send us that. Just > copy and paste the text directly into the email. This is > *much* more useful for us. > > cheers > Bruce > > > On Fri, 25 Jan 2019, Amrita Bedi wrote: > > > External Email - Use Caution > > > [0a440090-c896-4f22-8bd2-fe98f24c8013] > On Friday, January 25, 2019, Amrita Bedi > <amibedi273@gmail.com <mailto:amibedi273@gmail.com> <mailto:amibedi273@gmail.com <mailto:amibedi273@gmail.com>>> wrote: > [IMAGE] > Here you go. > On Friday, January 25, 2019, Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > wrote: > Hi Amrita, can you just paste the text into > the email? > thanks > doug > > On 1/25/19 10:51 AM, Amrita Bedi wrote: > > External Email - Use Caution > > Hi Dr Greve, > Ran mris_fwhm and got the attached. > > On Thursday, January 24, 2019, Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > wrote: > Based on the output below, it looks like there are > problems with running > one of the freesurfer binaries. Can you run > mris_fwhm ? Just type the > command and return and see what happens. > > > > /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm > --mask > > /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_recon/Bold1/fc.lpccseed.surf.lh/mask.nii.gz > --i > > /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_recon/Bold1/fc.lpccseed.surf.lh/rho1mn.nii.gz > --o > > /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_recon/Bold1/fc.lpccseed.surf.lh/rho1mn.sm.nii.gz > --fwhm 20.000000 --smooth-only --s fsaverage --hemi > lh --sd > /share/VA_Imaging/Projects/salat/2389_TRT/abedi > /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm: > > /home/apps/matlab/MATLAB/R2011b/sys/os/glnxa64/libstdc++.so.6: > version > `GLIBCXX_3.4.11' not found (required by > /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm) > > > > On 1/23/19 10:11 AM, Amrita Bedi wrote: > > > > External Email - Use Caution > > > > Hi Dr Greve, > > > > Attached is the log file. > > > > On Tuesday, January 22, 2019, Greve, Douglas N.,Ph.D. > > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> wrote: > > > > Can you send the full terminal output and/or > the log file? > > > > On 1/22/19 2:53 PM, Amrita Bedi wrote: > > > > > > External Email - Use Caution > > > > > > Hello Freesurfer developers, > > > > > > I was following the functional connectivity > walkthrough for resting > > > stage BOLD data and I got the attached error > when I ran step 8 > > > (selxavg3-sess). Does anyone have any > thoughts on how to trouble > > shoot > > > this? > > > Not sure if it’s of any use but I ran this > using Freesurfer 6.0 on > > > Centos 7.4 > > > > > > Thank You. > > > > > > Best > > > Amrita > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <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> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <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> > <mailto: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> > <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> > <mailto: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> > <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> > <mailto: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> > <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> _______________________________________________ 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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