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. <
dgr...@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* <amibedi...@gmail.com <mailto:amibedi...@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>>
> >
> >
> > 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 <amibedi...@gmail.com
> > <mailto:amibedi...@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
> > <fis...@nmr.mgh.harvard.edu <mailto:fis...@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
> > <amibedi...@gmail.com <mailto:amibedi...@gmail.com>> wrote:
> > [IMAGE]
> > Here you go.
> > On Friday, January 25, 2019, Greve, Douglas N.,Ph.D.
> > <dgr...@mgh.harvard.edu <mailto:dgr...@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.
> > <dgr...@mgh.harvard.edu <mailto:dgr...@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.
> > > <dgr...@mgh.harvard.edu
> > <mailto:dgr...@mgh.harvard.edu>
> > <mailto:dgr...@mgh.harvard.edu
> > <mailto:dgr...@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
> > > >
> > > > ______________________________
> _________________
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> > > >
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> freesurfer>
> > >
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> freesurfer
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> freesurfer>>
> > >
> > >
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> freesurfer
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> freesurfer>>
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