Hi Doug,
I created a new first level analysis along with new contrasts and event numbers for a group of subjects I had previously done analyses on. All but one of the subjects finished selxavg3 without error, but one subject gave the following error:
Saving X matrix to /home/sidkundu/freesurfer/sessions/Heading-TTP/LMV2010_N19_Heading-TTP/bold/TTP-analysis-3/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf.
Error in cond (line 39) s = svd(A);
Error in fast_selxavg3 (line 248) XCond = cond(XtX);
ERROR: fast_selxavg3() failed\n
I looked at the generated Xtmp.mat file and it shows the design matrix X has all zeros in 2 columns, resulting in NaNs in the same columns for Xn, and corresponding NaNs in XtX. I'm wondering what would cause this or why it would only occur for only one subject.
_________________________________ Sid Kundu Biomedical Engineering Boston University
It's probably a problem with your design. Can you send me the Xtmp.mat file? doug
Sid Kundu wrote:
Hi Doug,
I created a new first level analysis along with new contrasts and event numbers for a group of subjects I had previously done analyses on. All but one of the subjects finished selxavg3 without error, but one subject gave the following error:
Saving X matrix to /home/sidkundu/freesurfer/sessions/Heading-TTP/LMV2010_N19_Heading-TTP/bold/TTP-analysis-3/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf.
Error in cond (line 39) s = svd(A);
Error in fast_selxavg3 (line 248) XCond = cond(XtX);
ERROR: fast_selxavg3() failed\n
I looked at the generated Xtmp.mat file and it shows the design matrix X has all zeros in 2 columns, resulting in NaNs in the same columns for Xn, and corresponding NaNs in XtX. I'm wondering what would cause this or why it would only occur for only one subject.
Sid Kundu Biomedical Engineering Boston University
It is attached. Finn mentioned it may be due to an event number being missing from the particular subject, which could be possible in the analysis I am doing. _________________________________ Sid Kundu Biomedical Engineering Boston University
On Thu, Mar 1, 2012 at 11:15 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
It's probably a problem with your design. Can you send me the Xtmp.mat file? doug
Sid Kundu wrote:
Hi Doug,
I created a new first level analysis along with new contrasts and event numbers for a group of subjects I had previously done analyses on. All but one of the subjects finished selxavg3 without error, but one subject gave the following error:
Saving X matrix to /home/sidkundu/freesurfer/** sessions/Heading-TTP/LMV2010_**N19_Heading-TTP/bold/TTP-** analysis-3/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf.
Error in cond (line 39) s = svd(A);
Error in fast_selxavg3 (line 248) XCond = cond(XtX);
------------------------------**------------
ERROR: fast_selxavg3() failed\n
I looked at the generated Xtmp.mat file and it shows the design matrix X has all zeros in 2 columns, resulting in NaNs in the same columns for Xn, and corresponding NaNs in XtX. I'm wondering what would cause this or why it would only occur for only one subject.
______________________________**___ Sid Kundu Biomedical Engineering Boston University
-- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://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/**compliancelinehttp://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.
If you have an event type for which there is no event, then that is definitely the problem. Let me know if it is not that. doug
Sid Kundu wrote:
It is attached. Finn mentioned it may be due to an event number being missing from the particular subject, which could be possible in the analysis I am doing. _________________________________ Sid Kundu Biomedical Engineering Boston University
On Thu, Mar 1, 2012 at 11:15 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
It's probably a problem with your design. Can you send me the Xtmp.mat file? doug Sid Kundu wrote: Hi Doug, I created a new first level analysis along with new contrasts and event numbers for a group of subjects I had previously done analyses on. All but one of the subjects finished selxavg3 without error, but one subject gave the following error: Saving X matrix to /home/sidkundu/freesurfer/sessions/Heading-TTP/LMV2010_N19_Heading-TTP/bold/TTP-analysis-3/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf. Error in cond (line 39) s = svd(A); Error in fast_selxavg3 (line 248) XCond = cond(XtX); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n I looked at the generated Xtmp.mat file and it shows the design matrix X has all zeros in 2 columns, resulting in NaNs in the same columns for Xn, and corresponding NaNs in XtX. I'm wondering what would cause this or why it would only occur for only one subject. _________________________________ Sid Kundu Biomedical Engineering Boston University -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel: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.
Hi Doug,
I'm having a similar problem. Subjects had the opportunity to classify stimuli into one of three categories (Good, Bad, Neutral). For some subjects, one of more of the runs did not contain any stimuli that they classified as Neutral. If I want to look at a contrast that compare Good-Neutral, how should I go about doing this with FS-FAST? I'd like to keep the runs that contained neutral classifications for those subjects, but if I have to throw out those subjects to get the contrast, I guess I could.
Thanks, Keith -- Keith Yoder PhD Student, Integrative Neuroscience Social Cognitive Neuroscience Laboratory The University of Chicago 5846 S. University Avenue, Kelly 312 Chicago, IL 60637 Phone: 574-215-9678 kjyoder@uchicago.edu
On Thu, Mar 1, 2012 at 2:27 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
If you have an event type for which there is no event, then that is definitely the problem. Let me know if it is not that. doug
Sid Kundu wrote:
It is attached. Finn mentioned it may be due to an event number being missing from the particular subject, which could be possible in the analysis I am doing. _________________________________ Sid Kundu Biomedical Engineering Boston University
On Thu, Mar 1, 2012 at 11:15 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
It's probably a problem with your design. Can you send me the Xtmp.mat file? doug Sid Kundu wrote: Hi Doug, I created a new first level analysis along with new contrasts and event numbers for a group of subjects I had previously done analyses on. All but one of the subjects finished selxavg3 without error, but one subject gave the following error: Saving X matrix to/home/sidkundu/freesurfer/sessions/Heading-TTP/LMV2010_N19_Heading-TTP/bold/TTP-analysis-3/Xtmp.mat
Error using svd Input to SVD must not contain NaN or Inf. Error in cond (line 39) s = svd(A); Error in fast_selxavg3 (line 248) XCond = cond(XtX); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n I looked at the generated Xtmp.mat file and it shows the design matrix X has all zeros in 2 columns, resulting in NaNs in the same columns for Xn, and corresponding NaNs in XtX. I'm wondering what would cause this or why it would only occur for only one subject. _________________________________ Sid Kundu Biomedical Engineering Boston University -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel: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.-- 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
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Hi Keith, if you don't have any Neutral in a session, you can't do a Good-Neutral comparison. If you have multiple runs within a session, then it should be ok. doug
On 12/07/2012 03:02 PM, Keith Yoder wrote:
Hi Doug,
I'm having a similar problem. Subjects had the opportunity to classify stimuli into one of three categories (Good, Bad, Neutral). For some subjects, one of more of the runs did not contain any stimuli that they classified as Neutral. If I want to look at a contrast that compare Good-Neutral, how should I go about doing this with FS-FAST? I'd like to keep the runs that contained neutral classifications for those subjects, but if I have to throw out those subjects to get the contrast, I guess I could.
Thanks, Keith -- Keith Yoder PhD Student, Integrative Neuroscience Social Cognitive Neuroscience Laboratory The University of Chicago 5846 S. University Avenue, Kelly 312 Chicago, IL 60637 Phone: 574-215-9678 kjyoder@uchicago.edu mailto:kjyoder@uchicago.edu
On Thu, Mar 1, 2012 at 2:27 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
If you have an event type for which there is no event, then that is definitely the problem. Let me know if it is not that. doug Sid Kundu wrote: > It is attached. Finn mentioned it may be due to an event number being > missing from the particular subject, which could be possible in the > analysis I am doing. > _________________________________ > Sid Kundu > Biomedical Engineering > Boston University > > > > On Thu, Mar 1, 2012 at 11:15 AM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > It's probably a problem with your design. Can you send me the > Xtmp.mat file? > doug > > > Sid Kundu wrote: > > Hi Doug, > > I created a new first level analysis along with new contrasts > and event numbers for a group of subjects I had previously > done analyses on. All but one of the subjects finished > selxavg3 without error, but one subject gave the following error: > > > Saving X matrix to > /home/sidkundu/freesurfer/sessions/Heading-TTP/LMV2010_N19_Heading-TTP/bold/TTP-analysis-3/Xtmp.mat > Error using svd > Input to SVD must not contain NaN or Inf. > > Error in cond (line 39) > s = svd(A); > > Error in fast_selxavg3 (line 248) > XCond = cond(XtX); > >> ------------------------------------------ > ERROR: fast_selxavg3() failed\n > > > I looked at the generated Xtmp.mat file and it shows the > design matrix X has all zeros in 2 columns, resulting in NaNs > in the same columns for Xn, and corresponding NaNs in XtX. I'm > wondering what would cause this or why it would only occur for > only one subject. > > _________________________________ > Sid Kundu > Biomedical Engineering > Boston University > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://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> > <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. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel: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> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Ah, the subject was missing Neutral from all three runs. Removing them from the sessid gets rid of the error.
Thanks! Keith -- Keith Yoder PhD Student, Integrative Neuroscience Social Cognitive Neuroscience Laboratory The University of Chicago 5846 S. University Avenue, Kelly 312 Chicago, IL 60637 Phone: 574-215-9678 kjyoder@uchicago.edu
On Fri, Dec 7, 2012 at 2:05 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Hi Keith, if you don't have any Neutral in a session, you can't do a Good-Neutral comparison. If you have multiple runs within a session, then it should be ok. doug
On 12/07/2012 03:02 PM, Keith Yoder wrote:
Hi Doug,
I'm having a similar problem. Subjects had the opportunity to classify stimuli into one of three categories (Good, Bad, Neutral). For some subjects, one of more of the runs did not contain any stimuli that they classified as Neutral. If I want to look at a contrast that compare Good-Neutral, how should I go about doing this with FS-FAST? I'd like to keep the runs that contained neutral classifications for those subjects, but if I have to throw out those subjects to get the contrast, I guess I could.
Thanks, Keith -- Keith Yoder PhD Student, Integrative Neuroscience Social Cognitive Neuroscience Laboratory The University of Chicago 5846 S. University Avenue, Kelly 312 Chicago, IL 60637 Phone: 574-215-9678 kjyoder@uchicago.edu mailto:kjyoder@uchicago.edu
On Thu, Mar 1, 2012 at 2:27 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>> wrote:
If you have an event type for which there is no event, then that is definitely the problem. Let me know if it is not that. doug Sid Kundu wrote: > It is attached. Finn mentioned it may be due to an event number being > missing from the particular subject, which could be possible in the > analysis I am doing. > ______________________________**___ > Sid Kundu > Biomedical Engineering > Boston University > > > > On Thu, Mar 1, 2012 at 11:15 AM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>>>wrote: > > It's probably a problem with your design. Can you send me the > Xtmp.mat file? > doug > > > Sid Kundu wrote: > > Hi Doug, > > I created a new first level analysis along with new contrasts > and event numbers for a group of subjects I had previously > done analyses on. All but one of the subjects finished > selxavg3 without error, but one subject gave the following error: > > > Saving X matrix to > /home/sidkundu/freesurfer/**sessions/Heading-TTP/LMV2010_** N19_Heading-TTP/bold/TTP-**analysis-3/Xtmp.mat > Error using svd > Input to SVD must not contain NaN or Inf. > > Error in cond (line 39) > s = svd(A); > > Error in fast_selxavg3 (line 248) > XCond = cond(XtX); > >> ------------------------------**------------ > ERROR: fast_selxavg3() failed\n > > > I looked at the generated Xtmp.mat file and it shows the > design matrix X has all zeros in 2 columns, resulting in NaNs > in the same columns for Xn, and corresponding NaNs in XtX. I'm > wondering what would cause this or why it would only occur for > only one subject. > > ______________________________**___ > Sid Kundu > Biomedical Engineering > Boston University > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>>
> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> <http://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> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> <http://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/**compliancelinehttp://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. > >
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu>Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://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> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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