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:
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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 > > > > _______________________________________________ > > 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> _______________________________________________ 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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