On Tuesday, January 29, 2019, Greve, Douglas N.,Ph.D. <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>>
> 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 <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>>
> 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>> wrote:
>    [IMAGE]
>    Here you go.
>    On Friday, January 25, 2019, Greve, Douglas N.,Ph.D.
> <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>>
> 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>>> 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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