[Freesurfer] Functional connectivty walkthrough step 8 error
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Functional connectivty walkthrough step 8 error
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> 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 > > 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 selxavg3-sess-Bold1-fc.lpccseed.surf.lh-190122151015.log Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Functional connectivty walkthrough step 8 error
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 20.00 --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. > > 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.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@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 > > 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
Re: [Freesurfer] Functional connectivty walkthrough step 8 error
External Email - Use Caution Here you go. On Friday, January 25, 2019, Greve, Douglas N.,Ph.D. 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 20.00 --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. >> > 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.edu/mailman/listinfo/freesurfer >> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> > >> > >> > ___ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh.har >> vard.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 >> > 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 > listfreesur...@nmr.mgh.harvard.eduhttps://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
Re: [Freesurfer] Functional connectivty walkthrough step 8 error
External Email - Use Caution On Friday, January 25, 2019, Amrita Bedi wrote: > > > 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 20.00 --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. >>> > 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.edu/mailman/listinfo/freesurfer >>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> > >>> > >>> > ___ >>> > Freesurfer mailing list >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh.har >>> vard.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 >>> > 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 >> listfreesur...@nmr.mgh.harvard.eduhttps://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
Re: [Freesurfer] Functional connectivty walkthrough step 8 error
External Email - Use Caution Pasted the text in the email but not sure if you can view it On Friday, January 25, 2019, Amrita Bedi wrote: > > > On Friday, January 25, 2019, Amrita Bedi wrote: > >> >> >> 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 20.00 --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. >>>> > 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.edu/mailman/listinfo/freesurfer >>>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>>> > >>>> > >>>> > ___ >>>> > Freesurfer mailing list >>>> > Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh.har >>>> vard.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 >>>> > 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 >>> listfreesur...@nmr.mgh.harvard.eduhttps://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
Re: [Freesurfer] Functional connectivty walkthrough step 8 error
External Email - Use Caution 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 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 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 20.00 --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. >> > 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/freesurfer >> > >> > >> > >> > ___ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@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 >> > 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
Re: [Freesurfer] Functional connectivty walkthrough step 8 error
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 --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 : 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 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 > 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 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 20.00 --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. >>> > 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 >>> > > >
[Freesurfer] Fwd: Functional connectivty walkthrough step 8 error
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 --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 : 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* Date: Friday, January 25, 2019 Subject: Functional connectivty walkthrough step 8 error To: Freesurfer support list 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 --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 : 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 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 > 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 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.
Re: [Freesurfer] Functional connectivty walkthrough step 8 error
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
> > --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 : 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* mailto:amibedi...@gmail.com>>
> > Date: Friday, January 25, 2019
> > Subject: Functional connectivty walkthrough step 8 error
> > To: Freesurfer support list > <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
> >--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 : 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 > <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
[Freesurfer] Fwd: Fw: mriglmfit error
External Email - Use Caution -- Forwarded message -- From: *abedi...@citymail.cuny.edu * < abedi...@citymail.cuny.edu> Date: Thursday, April 11, 2019 Subject: Fw: mriglmfit error To: Amrita Bedi Amrita Bedi *Biomedical Engineering - Class of 2018* *The City College of New York - CUNY* -- *From:* abedi...@citymail.cuny.edu *Sent:* Thursday, April 11, 2019 8:38 AM *To:* Freesurfer@nmr.mgh.harvard.edu *Subject:* mriglmfit error Good morning Freesurfer developers, While using the mri-glmfit command on 20 subjects. I got the following error- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit.bin --y test.10B.mgh --fsgd TEST.fsgd --C TEST.mtx --surf fsaverage lh --cortex --glmdir test.glmdir 2. The FSGD file (if using one) 3. And the design matrix above Attempting to diagnose further SumSq: Min=0.00 (col 6), Max=228.790298 (col 3) The scale is much different between columns 6 and 3, you may want to normalize by subtracting the mean and dividing by the standard deviation. Column 6, all values are 0. 1. My command line used was- mri_glmfit --y test.10B.mgh --fsgd TEST.fsgd --C TEST.mtx --surf fsaverage lh --cortex --glmdir test.glmdir 2. My fsgd file and design matrix file are attached. Thank you for your help. Amrita Bedi TEST.fsgd Description: Binary data Xg.dat Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Fw: mriglmfit error
External Email - Use Caution Hi Dr Greve, I can’t do the Fsgd in the DOSS format since it won’t be ok for my other 6 variables. I would appreciate it if you could guide me through it. Best Amrita On Thursday, April 11, 2019, Greve, Douglas N.,Ph.D. wrote: > Hi Amrita, first of all, thanks for following the instructions on > submitting the bug report! It helps us a lot to get all the information > the first time. As for your issue, there is a confound between the > Female class and the NSI_1 variable. All the Females have a NSI_1 value > of 0, meaning that you cannot compute a slope for the Females group. > What to do next depends a little on what you think is happening in the > data. You could run it with different-offset same-slope (mri_glmfit > --fsgd TEST.fsgd DOSS ...). This would force a single slope for both > males and females. This is not a problem for the NSI_1 variable because > there is no slope for females. If you think this is ok for CAPS_C, then > just do it. If not, then things get harder, but I can probably step you > through it. > > On 4/11/19 8:40 AM, Amrita Bedi wrote: > > > > External Email - Use Caution > > > > > > > > -- Forwarded message -- > > From: *abedi...@citymail.cuny.edu <mailto:abedi...@citymail.cuny.edu>* > > mailto:abedi...@citymail.cuny.edu>> > > Date: Thursday, April 11, 2019 > > Subject: Fw: mriglmfit error > > To: Amrita Bedi mailto:amibedi...@gmail.com>> > > > > > > > > > > Amrita Bedi > > /Biomedical Engineering - Class of 2018/ > > /The City College of New York - CUNY/ > > > > > > > > > > *From:* abedi...@citymail.cuny.edu <mailto:abedi...@citymail.cuny.edu> > > *Sent:* Thursday, April 11, 2019 8:38 AM > > *To:* Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > *Subject:* mriglmfit error > > > > Good morning Freesurfer developers, > > > > > > While using the mri-glmfit command on 20 subjects. I got the following > > error- > > > > > > ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 > > > > Possible problem with experimental design: > > Check for duplicate entries and/or lack of range of > > continuous variables within a class. > > If you seek help with this problem, make sure to send: > > 1. Your command line: > > mri_glmfit.bin --y test.10B.mgh --fsgd TEST.fsgd --C TEST.mtx > > --surf fsaverage lh --cortex --glmdir test.glmdir > > 2. The FSGD file (if using one) > > 3. And the design matrix above > > Attempting to diagnose further > > SumSq: Min=0.00 (col 6), Max=228.790298 (col 3) > > The scale is much different between columns 6 and 3, you may want to > > normalize by subtracting the mean and dividing by the standard > deviation. > > Column 6, all values are 0. > > > > 1. My command line used was- > > > > mri_glmfit --y test.10B.mgh --fsgd TEST.fsgd --C TEST.mtx --surf > > fsaverage lh --cortex --glmdir test.glmdir > > > > > > 2. My fsgd file and design matrix file are attached. > > > > Thank you for your help. > > > > > > > > > > Amrita Bedi > > > > > > > > > > ___ > > 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] Fwd: Fw: mriglmfit error
External Email - Use Caution Hi Dr Greve, Is the idea behind removing one column for the NS 1 column in the design matrix meant to remove the columns for females? And how do we know which of the two columns for the Ns_1 in the design matrix are for which gender? In the contrast (0 0 0 0 1-1) which column of the last two for the Ns_1 would be removed? For the DOSS, say it works for the Ns_1 since female scores for Ns_1 are 0 and we can say that the males and females are decreasing/increasing at the same rate. Would it be right to make the same assumption for Caps_c even though the caps score for females or males are not 0? Best Amrita -- Forwarded message -- From: *Greve, Douglas N.,Ph.D.* Date: Thursday, April 11, 2019 Subject: Fw: mriglmfit error To: "freesurfer@nmr.mgh.harvard.edu" In that case, you will have to create your own design matrix. The easiest way to do that is to start with the DODS Xg.dat matrix that you sent. There will be two columns for the NSI_1 variable (one for males, one for females). You need to reduce it down to one column. In the Xg.dat that you sent, the two columns are the last two columns; in this case, you can just remove the last column. Your contrast matrix will then need one less column. On 4/11/19 2:08 PM, Amrita Bedi wrote: > > External Email - Use Caution > > Hi Dr Greve, > > I can’t do the Fsgd in the DOSS format since it won’t be ok for my > other 6 variables. I would appreciate it if you could guide me through it. > > Best > Amrita > > On Thursday, April 11, 2019, Greve, Douglas N.,Ph.D. > mailto:dgr...@mgh.harvard.edu>> wrote: > > Hi Amrita, first of all, thanks for following the instructions on > submitting the bug report! It helps us a lot to get all the > information > the first time. As for your issue, there is a confound between the > Female class and the NSI_1 variable. All the Females have a NSI_1 > value > of 0, meaning that you cannot compute a slope for the Females group. > What to do next depends a little on what you think is happening in > the > data. You could run it with different-offset same-slope (mri_glmfit > --fsgd TEST.fsgd DOSS ...). This would force a single slope for both > males and females. This is not a problem for the NSI_1 variable > because > there is no slope for females. If you think this is ok for CAPS_C, > then > just do it. If not, then things get harder, but I can probably > step you > through it. > > On 4/11/19 8:40 AM, Amrita Bedi wrote: > > > > External Email - Use Caution > > > > > > > > -- Forwarded message -- > > From: *abedi...@citymail.cuny.edu > <mailto:abedi...@citymail.cuny.edu> > <mailto:abedi...@citymail.cuny.edu > <mailto:abedi...@citymail.cuny.edu>>* > > mailto:abedi...@citymail.cuny.edu> > <mailto:abedi...@citymail.cuny.edu > <mailto:abedi...@citymail.cuny.edu>>> > > Date: Thursday, April 11, 2019 > > Subject: Fw: mriglmfit error > > To: Amrita Bedi <mailto:amibedi...@gmail.com> <mailto:amibedi...@gmail.com > <mailto:amibedi...@gmail.com>>> > > > > > > > > > > Amrita Bedi > > /Biomedical Engineering - Class of 2018/ > > /The City College of New York - CUNY/ > > > > > > > > > > > *From:* abedi...@citymail.cuny.edu > <mailto:abedi...@citymail.cuny.edu> > <mailto:abedi...@citymail.cuny.edu > <mailto:abedi...@citymail.cuny.edu>> > > *Sent:* Thursday, April 11, 2019 8:38 AM > > *To:* Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > *Subject:* mriglmfit error > > > > Good morning Freesurfer developers, > > > > > > While using the mri-glmfit command on 20 subjects. I got the > following > > error- > > > > > > ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 > > > > Possible problem with experimental design: > > Check for duplicate entries and/or lack of range of > > continuous variables within a class. > > If you seek help with this problem, make sure to send: > > 1. Your command line: >
[Freesurfer] Fw: mriglmfit error
External Email - Use Caution Hi Dr Greve, Is the idea behind removing one column for the NS 1 column in the design matrix meant to remove the columns for females? And how do we know which of the two columns for the Ns_1 in the design matrix are for which gender? In the contrast (0 0 0 0 1-1) which column of the last two for the Ns_1 would be removed? For the DOSS, say it works for the caps score since female scores for Ns_1 are 0 and we can say that the -- Forwarded message -- From: *Greve, Douglas N.,Ph.D.* Date: Thursday, April 11, 2019 Subject: Fw: mriglmfit error To: "freesurfer@nmr.mgh.harvard.edu" In that case, you will have to create your own design matrix. The easiest way to do that is to start with the DODS Xg.dat matrix that you sent. There will be two columns for the NSI_1 variable (one for males, one for females). You need to reduce it down to one column. In the Xg.dat that you sent, the two columns are the last two columns; in this case, you can just remove the last column. Your contrast matrix will then need one less column. On 4/11/19 2:08 PM, Amrita Bedi wrote: > > External Email - Use Caution > > Hi Dr Greve, > > I can’t do the Fsgd in the DOSS format since it won’t be ok for my > other 6 variables. I would appreciate it if you could guide me through it. > > Best > Amrita > > On Thursday, April 11, 2019, Greve, Douglas N.,Ph.D. > mailto:dgr...@mgh.harvard.edu>> wrote: > > Hi Amrita, first of all, thanks for following the instructions on > submitting the bug report! It helps us a lot to get all the > information > the first time. As for your issue, there is a confound between the > Female class and the NSI_1 variable. All the Females have a NSI_1 > value > of 0, meaning that you cannot compute a slope for the Females group. > What to do next depends a little on what you think is happening in > the > data. You could run it with different-offset same-slope (mri_glmfit > --fsgd TEST.fsgd DOSS ...). This would force a single slope for both > males and females. This is not a problem for the NSI_1 variable > because > there is no slope for females. If you think this is ok for CAPS_C, > then > just do it. If not, then things get harder, but I can probably > step you > through it. > > On 4/11/19 8:40 AM, Amrita Bedi wrote: > > > > External Email - Use Caution > > > > > > > > -- Forwarded message -- > > From: *abedi...@citymail.cuny.edu > <mailto:abedi...@citymail.cuny.edu> > <mailto:abedi...@citymail.cuny.edu > <mailto:abedi...@citymail.cuny.edu>>* > > mailto:abedi...@citymail.cuny.edu> > <mailto:abedi...@citymail.cuny.edu > <mailto:abedi...@citymail.cuny.edu>>> > > Date: Thursday, April 11, 2019 > > Subject: Fw: mriglmfit error > > To: Amrita Bedi <mailto:amibedi...@gmail.com> <mailto:amibedi...@gmail.com > <mailto:amibedi...@gmail.com>>> > > > > > > > > > > Amrita Bedi > > /Biomedical Engineering - Class of 2018/ > > /The City College of New York - CUNY/ > > > > > > > > > --- - > > *From:* abedi...@citymail.cuny.edu > <mailto:abedi...@citymail.cuny.edu> > <mailto:abedi...@citymail.cuny.edu > <mailto:abedi...@citymail.cuny.edu>> > > *Sent:* Thursday, April 11, 2019 8:38 AM > > *To:* Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > *Subject:* mriglmfit error > > > > Good morning Freesurfer developers, > > > > > > While using the mri-glmfit command on 20 subjects. I got the > following > > error- > > > > > > ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 > > > > Possible problem with experimental design: > > Check for duplicate entries and/or lack of range of > > continuous variables within a class. > > If you seek help with this problem, make sure to send: > > 1. Your command line: > > mri_glmfit.bin --y test.10B.mgh --fsgd TEST.fsgd --C TEST.mtx > > --surf fsaverage lh --cortex --glmdir test.glmdir > > 2. The FSGD file (if using
[Freesurfer] fsgd creation
External Email - Use Caution Hi Freesurfer developers, My question is related to creation of an fsgd file for glm analysis. I have approximately 500 subjects and 10 variables. I was wondering whats the most time efficient way of creating an fsgd file given my data currently resides in an excel file. Best Amrita ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Mri glmfit sim error
External Email - Use Caution -- Forwarded message -- From: *abedi...@citymail.cuny.edu * < abedi...@citymail.cuny.edu> Date: Tuesday, May 21, 2019 Subject: To: "amibedi...@gmail.com" Hi Freesurfer developers, While running the mri glmfit sim command for a smoothing of 30 FWHM, I got the following error- Original mri_glmfit command line: cmdline mri_glmfit.bin --y lh.BINGE15.g2v1.30B.mgh --fsgd BINGE15.g2v1.txt dods --C BINGE.g2v1.group-x-LDH_age.mtx --surf fsaverage lh --cortex --glmdir lh.BINGE15_g2v1.group-x-LDH_age.30B.glmdir DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 53.156463 ERROR: cannot find /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/ cortex/fwhm53/abs/th13/mc-z.csd I researched on the Freesurfer wiki page and found Dr Greve answered a similar question saying-"When running mri_glmfit-sim, add --cache-dir /path/to/mult-comp-cor" but I dont understand. What is this path? Thank You! Best, Amrita ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Mri glmfit sim error
External Email - Use Caution Hi Dr Greve, Is it not possible to use Monte Carlo for 30 FWHM? Best, Amrita On Tuesday, May 21, 2019, Greve, Douglas N.,Ph.D. wrote: > You have applied a lot of smoothing, and the tables don't go up that high. > Usually people will apply 5-10mm of smoothing. If you really want that much > smoothing, you should use permutation. See https://surfer.nmr.mgh. > harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm > > On 5/21/2019 10:09 AM, Amrita Bedi wrote: > > External Email - Use Caution > > > -- Forwarded message -- > From: *abedi...@citymail.cuny.edu * < > abedi...@citymail.cuny.edu> > Date: Tuesday, May 21, 2019 > Subject: > To: "amibedi...@gmail.com" > > > Hi Freesurfer developers, > > While running the mri glmfit sim command for a smoothing of 30 FWHM, I got > the following error- > > Original mri_glmfit command line: > cmdline mri_glmfit.bin --y lh.BINGE15.g2v1.30B.mgh --fsgd BINGE15.g2v1.txt > dods --C BINGE.g2v1.group-x-LDH_age.mtx --surf fsaverage lh --cortex > --glmdir lh.BINGE15_g2v1.group-x-LDH_age.30B.glmdir > > DoSim = 0 > UseCache = 1 > DoPoll = 0 > DoPBSubmit = 0 > DoBackground = 0 > DiagCluster = 0 > gd2mtx = dods > fwhm = 53.156463 > ERROR: cannot find /usr/local/freesurfer/average/ > mult-comp-cor/fsaverage/lh/cortex/fwhm53/abs/th13/mc-z.csd > > > I researched on the Freesurfer wiki page and found Dr Greve answered a > similar question saying-"When running mri_glmfit-sim, add --cache-dir > /path/to/mult-comp-cor" but I dont understand. What is this path? > > Thank You! > > Best, > Amrita > > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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] Viewing clusters regardless of significance
External Email - Use Caution Hi Freesurfer developers, I’m using the glmfit tutorial to see clusters for my data. I’m trying to view the uncorrected clusters on tksuefer using the command line tksurfer fsaverage lh inflated -overlay /path to data/cache.th13.abs.sig.ocn.annot but don’t see any clusters. According to the cluster summary file there should be 2 clusters on the left hemisphere and 9 on the right. Thank you for your help. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Fwd: Fw: glm error
External Email - Use Caution -- Forwarded message -- From: *abedi...@citymail.cuny.edu * < abedi...@citymail.cuny.edu> Date: Thursday, October 31, 2019 Subject: Fw: glm error To: Amrita Bedi Amrita Bedi *Biomedical Engineering - Class of 2018* *The City College of New York - CUNY* -- *From:* abedi...@citymail.cuny.edu *Sent:* Thursday, October 31, 2019 12:02 PM *To:* Freesurfer@nmr.mgh.harvard.edu *Subject:* glm error Hello Freesurfer developers, I ran a seed based resting stage functional analysis for 287 subjects using the isthmus of the cingulate as a seed and now have pcc.nii.gz files in each individual subject folder. I concatenated these pcc files and am trying to run an osgm but get the following error: ERROR: DOF = 0 The commands i ran for concatenating and glm are: for l in `cat sessidBOLD2`; do mri_concat --o 4D_VOLUME_OUTPUT.lh.nii.gz --i $l/Bold/PCC_Bold1_L/bilat*/pcc.nii.gz; done mri_glmfit --y 4D_VOLUME_OUTPUT.lh.nii.gz --osgm --surf fsaverage lh --cortex --label /run/media/amritabedilocal/DATA/Amrita/2389/abedi /FSFAST_1to547_TR3/fsaverage/label/lh.cortex.label --glmdir all_subjects_lh_ic_pcc.TR3.glmdir The mriglmfit.log gave me the following: $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_ 1to547_TR3/FSFAST cmdline mri_glmfit --y 4D_VOLUME_OUTPUT.lh.nii.gz --osgm --surf fsaverage lh --cortex --label /run/media/amritabedilocal/ DATA/Amrita/2389/abedi/FSFAST_1to547_TR3/fsaverage/label/lh.cortex.label --glmdir all_subjects_lh_ic_pcc.TR3.glmdir sysname Linux hostname imaging5.vaboston.lan machine x86_64 user root FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y/run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_ 1to547_TR3/FSFAST/4D_VOLUME_OUTPUT.lh.nii.gz logyflag 0 usedti 0 labelmask /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_ 1to547_TR3/fsaverage/label/lh.cortex.label maskinv 0 glmdir all_subjects_lh_ic_pcc.TR3.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Thank you for your help. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Fw: glm error
External Email - Use Caution Thank you Dr Greve, that issue is resolved. I do have another question. I’m now trying to extract mean correlation values to the seed from each individual subject and not sure how to go about this. On Thursday, October 31, 2019, Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > You are not creating the 4D_VOLUME_OUTPUT.lh.nii.gz file correctly > Try > mri_concat --o 4D_VOLUME_OUTPUT.lh.nii.gz --i > */Bold/PCC_Bold1_L/bilat*/pcc.nii.gz > > Where you have "bilat*", that should only be one folder > > > On 10/31/19 12:04 PM, Amrita Bedi wrote: > > > > External Email - Use Caution > > > > > > > > -- Forwarded message -- > > From: *abedi...@citymail.cuny.edu <mailto:abedi...@citymail.cuny.edu>* > > mailto:abedi...@citymail.cuny.edu>> > > Date: Thursday, October 31, 2019 > > Subject: Fw: glm error > > To: Amrita Bedi mailto:amibedi...@gmail.com>> > > > > > > > > > > Amrita Bedi > > /Biomedical Engineering - Class of 2018/ > > /The City College of New York - CUNY/ > > > > > > *From:* abedi...@citymail.cuny.edu <mailto:abedi...@citymail.cuny.edu> > > *Sent:* Thursday, October 31, 2019 12:02 PM > > *To:* Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > mailto:Freesurfer@nmr.mgh.harvard.edu>> > > *Subject:* glm error > > Hello Freesurfer developers, > > > > I ran a seed based resting stage functional analysis for 287 subjects > > using the isthmus of the cingulate as a seed and now have pcc.nii.gz > > files in each individual subject folder. I concatenated these pcc > > files and am trying to run an osgm but get the following error: > > ERROR: DOF = 0 > > The commands i ran for concatenating and glm are: > > for l in `cat sessidBOLD2`; do mri_concat --o > > 4D_VOLUME_OUTPUT.lh.nii.gz --i $l/Bold/PCC_Bold1_L/bilat*/pcc.nii.gz; > done > > > > mri_glmfit --y 4D_VOLUME_OUTPUT.lh.nii.gz --osgm --surf fsaverage lh > > --cortex --label /run/media/amritabedilocal/DATA/Amrita/2389/abedi > > /FSFAST_1to547_TR3/fsaverage/label/lh.cortex.label --glmdir > > all_subjects_lh_ic_pcc.TR3.glmdir > > > > The mriglmfit.log gave me the following: > > > > > > $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ > > cwd > > /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_ > 1to547_TR3/FSFAST > > cmdline mri_glmfit --y 4D_VOLUME_OUTPUT.lh.nii.gz --osgm --surf > > fsaverage lh --cortex --label > > /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_ > 1to547_TR3/fsaverage/label/lh.cortex.label > > --glmdir all_subjects_lh_ic_pcc.TR3.glmdir > > sysname Linux > > hostname imaging5.vaboston.lan > > machine x86_64 > > user root > > FixVertexAreaFlag = 1 > > UseMaskWithSmoothing 1 > > OneSampleGroupMean 1 > > y > > /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_ > 1to547_TR3/FSFAST/4D_VOLUME_OUTPUT.lh.nii.gz > > logyflag 0 > > usedti 0 > > labelmask > > /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_ > 1to547_TR3/fsaverage/label/lh.cortex.label > > maskinv 0 > > glmdir all_subjects_lh_ic_pcc.TR3.glmdir > > IllCondOK 0 > > ReScaleX 1 > > DoFFx 0 > > > > Thank you for your help. > > > > > > ___ > > 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
Re: [Freesurfer] Fw: glm error
External Email - Use Caution Mean correlation values to the seed from activations of a pcc.mgh map from each individual subject. On Thursday, October 31, 2019, Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > mean over what? a parcellation? an activation cluster? > > On 10/31/2019 3:15 PM, Amrita Bedi wrote: > > External Email - Use Caution > Thank you Dr Greve, that issue is resolved. > > I do have another question. I’m now trying to extract mean correlation > values to the seed from each individual subject and not sure how to go > about this. > > On Thursday, October 31, 2019, Greve, Douglas N.,Ph.D. < > dgr...@mgh.harvard.edu> wrote: > >> You are not creating the 4D_VOLUME_OUTPUT.lh.nii.gz file correctly >> Try >> mri_concat --o 4D_VOLUME_OUTPUT.lh.nii.gz --i >> */Bold/PCC_Bold1_L/bilat*/pcc.nii.gz >> >> Where you have "bilat*", that should only be one folder >> >> >> On 10/31/19 12:04 PM, Amrita Bedi wrote: >> > >> > External Email - Use Caution >> > >> > >> > >> > -- Forwarded message -- >> > From: *abedi...@citymail.cuny.edu <mailto:abedi...@citymail.cuny.edu>* >> > mailto:abedi...@citymail.cuny.edu>> >> > Date: Thursday, October 31, 2019 >> > Subject: Fw: glm error >> > To: Amrita Bedi mailto:amibedi...@gmail.com>> >> > >> > >> > >> > >> > Amrita Bedi >> > /Biomedical Engineering - Class of 2018/ >> > /The City College of New York - CUNY/ >> > >> > >> >> > *From:* abedi...@citymail.cuny.edu <mailto:abedi...@citymail.cuny.edu> >> > *Sent:* Thursday, October 31, 2019 12:02 PM >> > *To:* Freesurfer@nmr.mgh.harvard.edu >> > <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > mailto:Freesurfer@nmr.mgh.harvard.edu >> >> >> > *Subject:* glm error >> > Hello Freesurfer developers, >> > >> > I ran a seed based resting stage functional analysis for 287 subjects >> > using the isthmus of the cingulate as a seed and now have pcc.nii.gz >> > files in each individual subject folder. I concatenated these pcc >> > files and am trying to run an osgm but get the following error: >> > ERROR: DOF = 0 >> > The commands i ran for concatenating and glm are: >> > for l in `cat sessidBOLD2`; do mri_concat --o >> > 4D_VOLUME_OUTPUT.lh.nii.gz --i $l/Bold/PCC_Bold1_L/bilat*/pcc.nii.gz; >> done >> > >> > mri_glmfit --y 4D_VOLUME_OUTPUT.lh.nii.gz --osgm --surf fsaverage lh >> > --cortex --label /run/media/amritabedilocal/DATA/Amrita/2389/abedi >> > /FSFAST_1to547_TR3/fsaverage/label/lh.cortex.label --glmdir >> > all_subjects_lh_ic_pcc.TR3.glmdir >> > >> > The mriglmfit.log gave me the following: >> > >> > >> > $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ >> > cwd >> > /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1to >> 547_TR3/FSFAST >> > cmdline mri_glmfit --y 4D_VOLUME_OUTPUT.lh.nii.gz --osgm --surf >> > fsaverage lh --cortex --label >> > /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1to >> 547_TR3/fsaverage/label/lh.cortex.label >> > --glmdir all_subjects_lh_ic_pcc.TR3.glmdir >> > sysname Linux >> > hostname imaging5.vaboston.lan >> > machine x86_64 >> > user root >> > FixVertexAreaFlag = 1 >> > UseMaskWithSmoothing 1 >> > OneSampleGroupMean 1 >> > y >> > /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1t >> o547_TR3/FSFAST/4D_VOLUME_OUTPUT.lh.nii.gz >> > logyflag 0 >> > usedti 0 >> > labelmask >> > /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1t >> o547_TR3/fsaverage/label/lh.cortex.label >> > maskinv 0 >> > glmdir all_subjects_lh_ic_pcc.TR3.glmdir >> > IllCondOK 0 >> > ReScaleX 1 >> > DoFFx 0 >> > >> > Thank you for your help. >> > >> > >> > ___ >> > 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 > listfreesur...@nmr.mgh.harvard.eduhttps://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
Re: [Freesurfer] Fw: glm error
External Email - Use Caution Across all activations since the pcc map was generated by an osgm. On Friday, November 1, 2019, Greve, Douglas N.,Ph.D. wrote: > you mean the average across all activations or clusters of activation? > > On 10/31/2019 9:18 PM, Amrita Bedi wrote: > > External Email - Use Caution > Mean correlation values to the seed from activations of a pcc.mgh map from > each individual subject. > > On Thursday, October 31, 2019, Greve, Douglas N.,Ph.D. < > dgr...@mgh.harvard.edu> wrote: > >> mean over what? a parcellation? an activation cluster? >> >> On 10/31/2019 3:15 PM, Amrita Bedi wrote: >> >> External Email - Use Caution >> Thank you Dr Greve, that issue is resolved. >> >> I do have another question. I’m now trying to extract mean correlation >> values to the seed from each individual subject and not sure how to go >> about this. >> >> On Thursday, October 31, 2019, Greve, Douglas N.,Ph.D. < >> dgr...@mgh.harvard.edu> wrote: >> >>> You are not creating the 4D_VOLUME_OUTPUT.lh.nii.gz file correctly >>> Try >>> mri_concat --o 4D_VOLUME_OUTPUT.lh.nii.gz --i >>> */Bold/PCC_Bold1_L/bilat*/pcc.nii.gz >>> >>> Where you have "bilat*", that should only be one folder >>> >>> >>> On 10/31/19 12:04 PM, Amrita Bedi wrote: >>> > >>> > External Email - Use Caution >>> > >>> > >>> > >>> > -- Forwarded message ------ >>> > From: *abedi...@citymail.cuny.edu <mailto:abedi...@citymail.cuny.edu>* >>> >>> > mailto:abedi...@citymail.cuny.edu>> >>> > Date: Thursday, October 31, 2019 >>> > Subject: Fw: glm error >>> > To: Amrita Bedi mailto:amibedi...@gmail.com>> >>> > >>> > >>> > >>> > >>> > Amrita Bedi >>> > /Biomedical Engineering - Class of 2018/ >>> > /The City College of New York - CUNY/ >>> > >>> > >>> >>> > *From:* abedi...@citymail.cuny.edu <mailto:abedi...@citymail.cuny.edu> >>> > *Sent:* Thursday, October 31, 2019 12:02 PM >>> > *To:* Freesurfer@nmr.mgh.harvard.edu >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> > mailto:Freesurfer@nmr.mgh.harvard.edu >>> >> >>> > *Subject:* glm error >>> > Hello Freesurfer developers, >>> > >>> > I ran a seed based resting stage functional analysis for 287 subjects >>> > using the isthmus of the cingulate as a seed and now have pcc.nii.gz >>> > files in each individual subject folder. I concatenated these pcc >>> > files and am trying to run an osgm but get the following error: >>> > ERROR: DOF = 0 >>> > The commands i ran for concatenating and glm are: >>> > for l in `cat sessidBOLD2`; do mri_concat --o >>> > 4D_VOLUME_OUTPUT.lh.nii.gz --i $l/Bold/PCC_Bold1_L/bilat*/pcc.nii.gz; >>> done >>> > >>> > mri_glmfit --y 4D_VOLUME_OUTPUT.lh.nii.gz --osgm --surf fsaverage lh >>> > --cortex --label /run/media/amritabedilocal/DATA/Amrita/2389/abedi >>> > /FSFAST_1to547_TR3/fsaverage/label/lh.cortex.label --glmdir >>> > all_subjects_lh_ic_pcc.TR3.glmdir >>> > >>> > The mriglmfit.log gave me the following: >>> > >>> > >>> > $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ >>> > cwd >>> > /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1to >>> 547_TR3/FSFAST >>> > cmdline mri_glmfit --y 4D_VOLUME_OUTPUT.lh.nii.gz --osgm --surf >>> > fsaverage lh --cortex --label >>> > /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1to >>> 547_TR3/fsaverage/label/lh.cortex.label >>> > --glmdir all_subjects_lh_ic_pcc.TR3.glmdir >>> > sysname Linux >>> > hostname imaging5.vaboston.lan >>> > machine x86_64 >>> > user root >>> > FixVertexAreaFlag = 1 >>> > UseMaskWithSmoothing 1 >>> > OneSampleGroupMean 1 >>> > y >>> > /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1t >>> o547_TR3/FSFAST/4D_VOLUME_OUTPUT.lh.nii.gz >>> > logyflag 0 >>> > usedti 0 >>> > labelmask >>> > /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1t >>> o547_TR3/fsaverage/label/lh.cortex.label >>> > maskinv 0 >>> > glmdir all_subjects_lh_ic_pcc.TR3.glmdir >>> > IllCondOK 0 >>> > ReScaleX 1 >>> > DoFFx 0 >>> > >>> > Thank you for your help. >>> > >>> > >>> > ___ >>> > 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 >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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] Mean thickness values from sig.mgh
External Email - Use Caution Hello Freesurfer developers, I wanted to extract mean thickness values of all participants from the uncorrected significance maps obtained from mri glmfit for structural data instead of extracting it from the corrected maps from glmfit sim. Is there a way to do this? Thank you. Amrita ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
