External Email - Use Caution 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> 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> > 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> wrote: >>> [IMAGE] >>> Here you go. >>> On Friday, January 25, 2019, Greve, Douglas N.,Ph.D. < >>> 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> 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_rec >>> on/Bold1/fc.lpccseed.surf.lh/mask.nii.gz >>> --i >>> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec >>> on/Bold1/fc.lpccseed.surf.lh/rho1mn.nii.gz >>> --o >>> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec >>> on/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>> 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> >>> > > https://mail.nmr.mgh.harvard.e >>> du/mailman/listinfo/freesurfer >>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurf >>> er> >>> > >>> > >>> > _______________________________________________ >>> > 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/freesurf >>> er> >>> > >>> > >>> > _______________________________________________ >>> > Freesurfer mailing list >>> > Freesurfer@nmr.mgh.harvard.edu >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>>
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
