Hello,
We are attempting to run an analysis using selxavg3-sess but keep getting an error.
We are using:
freesurfer v5
Our subjects directory: /cluster/manoach/milton/subjects
Command that was run:
selxavg3-sess -analysis mandylh2 -fwhm -s PAMST06
Output that was given:
Creating Design Matrix ... creation time = 0.006 sec DoMCFit = 1 ntptot = 250, nX = 5, DOF = 245 Saving X matrix to /autofs/cluster/manoach/milton/subjects/PAMST06/bold/mandylh2/Xtmp.mat ??? Error using ==> svd Input to SVD must not contain NaN or Inf.
Error in ==> cond at 40 s = svd(A);
Error in ==> fast_selxavg3 at 256 XCond = cond(XtX);
ERROR: fast_selxavg3() failed\n
Do you know what might cause this?
Thanks! --Mandy
Usually this means that there is something wrong with your design or paradigm files. CAn you send the paradigm files and the mkanalysis-sess command? doug
Mandy Nagy wrote:
Hello,
We are attempting to run an analysis using selxavg3-sess but keep getting an error.
We are using:
freesurfer v5
Our subjects directory: /cluster/manoach/milton/subjects
Command that was run:
selxavg3-sess -analysis mandylh2 -fwhm -s PAMST06
Output that was given:
Creating Design Matrix ... creation time = 0.006 sec DoMCFit = 1 ntptot = 250, nX = 5, DOF = 245 Saving X matrix to /autofs/cluster/manoach/milton/subjects/PAMST06/bold/mandylh2/Xtmp.mat ??? Error using ==> svd Input to SVD must not contain NaN or Inf.
Error in ==> cond at 40 s = svd(A);
Error in ==> fast_selxavg3 at 256 XCond = cond(XtX);
ERROR: fast_selxavg3() failed\n
Do you know what might cause this?
Thanks!
--Mandy
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Our mkanalysis-sess command:
mkanalysis-sess -analysis mandylh2 -surface fsaverage lh -fwhm 8 -event-related -paradigm paradigm.par -TR 3 -nconditions 2 -runlistfile task -gammafit 2.25 1.25 -refeventdur 30
Our paradigm file:
0 0 30 1 Rest 30 1 30 1 Typing 60 0 30 1 Rest 90 1 30 1 Typing 120 0 30 1 Rest 150 1 30 1 Typing 180 0 30 1 Rest 210 1 30 1 Typing 240 0 30 1 Rest 270 1 30 1 Typing 300 0 30 1 Rest 330 1 30 1 Typing 360 0 30 1 Rest 390 1 30 1 Typing 420 0 30 1 Rest 450 1 30 1 Typing 480 0 30 1 Rest 510 1 30 1 Typing 540 0 30 1 Rest 570 1 30 1 Typing 600 0 30 1 Rest 630 1 30 1 Typing 660 0 30 1 Rest 690 1 30 1 Typing 720 0 30 1 Rest
Thanks! --Mandy
On Mon, Feb 14, 2011 at 10:20 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
Usually this means that there is something wrong with your design or paradigm files. CAn you send the paradigm files and the mkanalysis-sess command? doug
Mandy Nagy wrote:
Hello,
We are attempting to run an analysis using selxavg3-sess but keep getting an error. We are using:
freesurfer v5
Our subjects directory: /cluster/manoach/milton/subjects
Command that was run:
selxavg3-sess -analysis mandylh2 -fwhm -s PAMST06
Output that was given:
Creating Design Matrix ... creation time = 0.006 sec DoMCFit = 1 ntptot = 250, nX = 5, DOF = 245 Saving X matrix to /autofs/cluster/manoach/milton/subjects/PAMST06/bold/mandylh2/Xtmp.mat ??? Error using ==> svd Input to SVD must not contain NaN or Inf.
Error in ==> cond at 40 s = svd(A);
Error in ==> fast_selxavg3 at 256 XCond = cond(XtX);
ERROR: fast_selxavg3() failed\n
Do you know what might cause this?
Thanks!
--Mandy
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
List the number of conditions as 1 (there is 1 non-null/rest/fixation condition).
doug
Mandy Nagy wrote:
Our mkanalysis-sess command:
mkanalysis-sess -analysis mandylh2 -surface fsaverage lh -fwhm 8 -event-related -paradigm paradigm.par -TR 3 -nconditions 2 -runlistfile task -gammafit 2.25 1.25 -refeventdur 30
Our paradigm file:
0 0 30 1 Rest 30 1 30 1 Typing 60 0 30 1 Rest 90 1 30 1 Typing 120 0 30 1 Rest 150 1 30 1 Typing 180 0 30 1 Rest 210 1 30 1 Typing 240 0 30 1 Rest 270 1 30 1 Typing 300 0 30 1 Rest 330 1 30 1 Typing 360 0 30 1 Rest 390 1 30 1 Typing 420 0 30 1 Rest 450 1 30 1 Typing 480 0 30 1 Rest 510 1 30 1 Typing 540 0 30 1 Rest 570 1 30 1 Typing 600 0 30 1 Rest 630 1 30 1 Typing 660 0 30 1 Rest 690 1 30 1 Typing 720 0 30 1 Rest
Thanks! --Mandy
On Mon, Feb 14, 2011 at 10:20 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Usually this means that there is something wrong with your design or paradigm files. CAn you send the paradigm files and the mkanalysis-sess command? doug Mandy Nagy wrote: Hello, We are attempting to run an analysis using selxavg3-sess but keep getting an error. We are using: freesurfer v5 Our subjects directory: /cluster/manoach/milton/subjects Command that was run: selxavg3-sess -analysis mandylh2 -fwhm -s PAMST06 Output that was given: Creating Design Matrix ... creation time = 0.006 sec DoMCFit = 1 ntptot = 250, nX = 5, DOF = 245 Saving X matrix to /autofs/cluster/manoach/milton/subjects/PAMST06/bold/mandylh2/Xtmp.mat ??? Error using ==> svd Input to SVD must not contain NaN or Inf. Error in ==> cond at 40 s = svd(A); Error in ==> fast_selxavg3 at 256 XCond = cond(XtX); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Do you know what might cause this? Thanks! --Mandy ------------------------------------------------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> 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 N Greve -
Mandy Nagy