Running the "selxavg3-sess -s" command line in FS-FAST for seed-based functional connectivity analysis
the following errors occurred:
--------------------------
Temporally filtering
Error using chol
Matrix must be positive definite.
Error in fast_selxavg3b (line 947)
Wseg = inv(chol(toeplitz(acfrun))');
--------------------------
Thanks
Stefano
What is your mkanalysis-sess command line?
On 12/28/17 8:53 AM, stdp82@virgilio.it wrote:
Running the "selxavg3-sess -s" command line in FS-FAST for seed-based functional connectivity analysis
the following errors occurred:
Temporally filtering
Error using chol
Matrix must be positive definite.
Error in fast_selxavg3b (line 947)
Wseg = inv(chol(toeplitz(acfrun))');
Thanks
Stefano
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
selxavg3-sess -sf sessid -a fc.rhamgseed.surf.rh
I have already used this command line many times, previously, using other labels. It has always worked well. I wonder if that error could be come from the update of my computer by macOS 1. Thanks Stefano
Il 31 dicembre 2017 alle 22.34 Douglas Greve greve@nmr.mgh.harvard.edu ha scritto:
What is your mkanalysis-sess command line? On 12/28/17 8:53 AM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > >Running the "selxavg3-sess -s" command line in FS-FAST for seed-based functional connectivity analysis the following errors occurred: -------------------------- Temporally filtering Error using chol Matrix must be positive definite. Error in fast_selxavg3b (line 947) Wseg = inv(chol(toeplitz(acfrun))'); -------------------------- Thanks Stefano _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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I meant your mkanalysis-sess command, not your selxavg3-sess command
On 1/1/18 12:36 PM, stdp82@virgilio.it wrote:
selxavg3-sess -sf sessid -a fc.rhamgseed.surf.rh
I have already used this command line many times, previously, using other labels. It has always worked well. I wonder if that error could be come from the update of my computer by macOS 1. Thanks Stefano
Il 31 dicembre 2017 alle 22.34 Douglas Greve greve@nmr.mgh.harvard.edu ha scritto:
What is your mkanalysis-sess command line?
On 12/28/17 8:53 AM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote:
Running the "selxavg3-sess -s" command line in FS-FAST for seed-based functional connectivity analysis
the following errors occurred:
Temporally filtering
Error using chol
Matrix must be positive definite.
Error in fast_selxavg3b (line 947)
Wseg = inv(chol(toeplitz(acfrun))');
Thanks
Stefano
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
mkanalysis-sess -analysis fc.lhamgseed.surf.lh -surface fsaverage lh -fwhm 6 -notask -taskreg L_Amygdala.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 3 -per-run -hpf 0.1 -lpf 0.01
Il 1 gennaio 2018 alle 18.49 Douglas Greve greve@nmr.mgh.harvard.edu ha scritto:
I meant your mkanalysis-sess command, not your selxavg3-sess command On 1/1/18 12:36 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > >selxavg3-sess -sf sessid -a fc.rhamgseed.surf.rh I have already used this command line many times, previously, using other labels. It has always worked well. I wonder if that error could be come from the update of my computer by macOS 1. Thanks Stefano > > > Il 31 dicembre 2017 alle 22.34 Douglas Greve <greve@nmr.mgh.harvard.edu> mailto:greve@nmr.mgh.harvard.edu ha scritto:What is your mkanalysis-sess command line? On 12/28/17 8:53 AM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > > > >Running the "selxavg3-sess -s" command line in FS-FAST for seed-based functional connectivity analysis the following errors occurred: -------------------------- Temporally filtering Error using chol Matrix must be positive definite. Error in fast_selxavg3b (line 947) Wseg = inv(chol(toeplitz(acfrun))'); -------------------------- Thanks Stefano _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. > >>
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mkanalysis-sess -analysis fc.lhamgseed.surf.lh -surface fsaverage lh -fwhm 6 -notask -taskreg L_Amygdala.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 3 -per-run -hpf 0.1 -lpf 0.01
Thanks
Il 31 dicembre 2017 alle 22.34 Douglas Greve greve@nmr.mgh.harvard.edu ha scritto:
What is your mkanalysis-sess command line? On 12/28/17 8:53 AM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > >Running the "selxavg3-sess -s" command line in FS-FAST for seed-based functional connectivity analysis the following errors occurred: -------------------------- Temporally filtering Error using chol Matrix must be positive definite. Error in fast_selxavg3b (line 947) Wseg = inv(chol(toeplitz(acfrun))'); -------------------------- Thanks Stefano _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
You need to swap the values of the hpf and lpf. The way you have it, you are essentially filtering out everything above .01 Hz, which probably leaves almost no signal
On 1/3/18 3:00 PM, stdp82@virgilio.it wrote:
mkanalysis-sess -analysis fc.lhamgseed.surf.lh -surface fsaverage lh -fwhm 6 -notask -taskreg L_Amygdala.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 3 -per-run -hpf 0.1 -lpf 0.01
Thanks
Il 31 dicembre 2017 alle 22.34 Douglas Greve greve@nmr.mgh.harvard.edu ha scritto:
What is your mkanalysis-sess command line?
On 12/28/17 8:53 AM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote:
Running the "selxavg3-sess -s" command line in FS-FAST for seed-based functional connectivity analysis
the following errors occurred:
Temporally filtering
Error using chol
Matrix must be positive definite.
Error in fast_selxavg3b (line 947)
Wseg = inv(chol(toeplitz(acfrun))');
Thanks
Stefano
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
I have done the changes did you suggested:
mkanalysis-sess -analysis fc.rhipposeed.mni305 -mni305 -fwhm 6 -notask -taskreg R_Hippocampus.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 3 -per-run -hpf 0.01 -lpf 0.1 -force
but the error persists:
GLS Beta Pass
run 1 t= 0.0
Temporally filtering
GLS Residual Pass
run 1 t= 0.0
Temporally filtering
Error using chol
Matrix must be positive definite.
Error in fast_selxavg3b (line 947)
Wseg = inv(chol(toeplitz(acfrun))');
IMPORTANT
Please take in account that before to update the MacOs system to version 11, the command run on the same data independently, if I choose -hpf 0.01 -lpf 0.1 or viceversa.
Il 5 gennaio 2018 alle 17.17 Douglas Greve greve@nmr.mgh.harvard.edu ha scritto:
You need to swap the values of the hpf and lpf. The way you have it, you are essentially filtering out everything above .01 Hz, which probably leaves almost no signal On 1/3/18 3:00 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > >mkanalysis-sess -analysis fc.lhamgseed.surf.lh -surface fsaverage lh -fwhm 6 -notask -taskreg L_Amygdala.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 3 -per-run -hpf 0.1 -lpf 0.01 Thanks > > > Il 31 dicembre 2017 alle 22.34 Douglas Greve <greve@nmr.mgh.harvard.edu> mailto:greve@nmr.mgh.harvard.edu ha scritto:What is your mkanalysis-sess command line? On 12/28/17 8:53 AM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > > > >Running the "selxavg3-sess -s" command line in FS-FAST for seed-based functional connectivity analysis the following errors occurred: -------------------------- Temporally filtering Error using chol Matrix must be positive definite. Error in fast_selxavg3b (line 947) Wseg = inv(chol(toeplitz(acfrun))'); -------------------------- Thanks Stefano _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. > >>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
stdp82＠virgilio.it