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
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
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> 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 CautionHello 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
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> 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: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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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> 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 CautionHi 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> 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: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 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
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.edumailto: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 CautionHi Dr Greve,
Attached is the log file.
On Tuesday, January 22, 2019, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edumailto: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> _______________________________________________ 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>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Here you go. On Friday, January 25, 2019, Greve, Douglas N.,Ph.D. 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 CautionHi Dr Greve,
Ran mris_fwhm and got the attached.
On Thursday, January 24, 2019, Greve, Douglas N.,Ph.D. < 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_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 CautionHi 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> 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 forresting
> 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: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 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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
On Friday, January 25, 2019, Amrita Bedi amibedi273@gmail.com wrote:
Here you go. On Friday, January 25, 2019, Greve, Douglas N.,Ph.D. < 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 CautionHi Dr Greve,
Ran mris_fwhm and got the attached.
On Thursday, January 24, 2019, Greve, Douglas N.,Ph.D. < 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_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 CautionHi 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> 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 forresting
> 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 6.0on
> 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: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 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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 amibedi273@gmail.com wrote:
On Friday, January 25, 2019, Amrita Bedi amibedi273@gmail.com wrote:
Here you go. On Friday, January 25, 2019, Greve, Douglas N.,Ph.D. < 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 CautionHi Dr Greve,
Ran mris_fwhm and got the attached.
On Thursday, January 24, 2019, Greve, Douglas N.,Ph.D. < 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_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 CautionHi 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> 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 forresting
> 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 6.0on
> 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: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 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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 wrote: [IMAGE] Here you go. On Friday, January 25, 2019, Greve, Douglas N.,Ph.D. 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 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>> 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: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 > 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
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 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 wrote: [IMAGE] Here you go. On Friday, January 25, 2019, Greve, Douglas N.,Ph.D. < 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> 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_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. > <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 forresting > > 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: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 > 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
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 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 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 wrote: [IMAGE] Here you go. On Friday, January 25, 2019, Greve, Douglas N.,Ph.D. < 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> 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_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. > <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 walkthroughfor 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
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 Date: Friday, January 25, 2019 Subject: Functional connectivty walkthrough step 8 error To: Freesurfer support list 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 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 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 wrote: [IMAGE] Here you go. On Friday, January 25, 2019, Greve, Douglas N.,Ph.D. < 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> 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_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. > <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 walkthroughfor 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
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 > > > > _______________________________________________ > > 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>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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. < 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 CautionHi 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>
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
The problem is that matlab is calling the mris_fwhm though a forked shell. When this shell starts up, it does not have the right environment. This is not easy for me to troubleshoot remotely. Do you have a linux system adminstrator who can help you?
On 1/30/19 10:26 AM, Amrita Bedi wrote:
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. <DGREVE@mgh.harvard.edu mailto: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> <mailto: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> > <mailto: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> > <mailto: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> <mailto: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> <mailto: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> <mailto: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> <mailto: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>> > <mailto: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>> > > <mailto: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>> > > > <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>> > <mailto: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>> > > > <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> > <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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I don't see anything.
On 1/25/19 11:56 AM, Amrita Bedi wrote:
External Email - Use Caution
[X]
Here you go. On Friday, January 25, 2019, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto: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.edumailto: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 CautionHi Dr Greve,
Attached is the log file.
On Tuesday, January 22, 2019, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edumailto: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> _______________________________________________ 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>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Amrita Bedi -
Bruce Fischl -
Greve, Douglas N.,Ph.D.