hi doug,

thank you so much for your quick reply.

yes - I saw this error after I sent you the error log. I checked the paradigm file, corrected it and rerun everything.

now this error is gone but I still get the following:

Error using svd Input to SVD must not contain NaN or Inf.

Error in cond (line 36) s = svd(A);

Error in fast_selxavg3 (line254) XCond = cond(XtX);

...

• • • • • — - - — - - — - — -

EROOR: fast_selxavg3() failed\n

Your help is much appreciated

On Dec 9, 2015, at 1:57 PM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:

Did you see the error description:

ERROR: /space/mdeh5/1/halgdev/projects/christina/FSFAST/Project/NC211_fmri_060515/Sess01/bold/004/oddeven.par is not correctly formatted. Line 19 only has 0 items

did you check this file?

On 12/09/2015 12:38 PM, Christina Pressl wrote: Dear Freesurfer Experts,

I am having trouble with selxavg3-sess and was wondering if you could maybe help me resolving the issue (error log attached)

I ran

#preproc-sess –s Sess01 –surface fsaverage lhrh –mni305 –fwhm 5 –per-run

and the following commands for lh, rh and mni305

#mkanalysis-sess –fsd bold –stc up -surface fsaverage lh -fwhm 5 -event-related -paradigm oddeven.par -nconditions 3 -spmhrf 0 -TR 2 -refeventdur 10.750 -nskip 4 –mcextreg -polyfit 2 -analysis oddeven.sm5.lh

#mkcontrast-sess –analysis oddeven.sm5.lh –contrast face-vs-object –a 1 –c 2 –c 3

#mkcontrast-sess –analysis oddeven.sm5.lh –contrast face-vs-fix –a 1 –c 0

Thank you very much.

Christina

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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto: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: https://gate.nmr.mgh.harvard.edu/filedrop2 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/

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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 see, here is a copy of my paradigm

0.0000 2 11.100 0 21.100 3 32.200 0 42.200 2 53.300 0 63.300 2 74.400 0 84.400 1 95.500 0 105.500 1 116.600 0 126.600 3 137.700 0 147.700 3 158.800 0 168.800 1 179.900 0

I don’t see how this setup reflects one of the two potential errors you outlined.

.par files are located separately in each run directory which are located in the bold directory.

thank you.

On Dec 9, 2015, at 2:22 PM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:

That means that your design matrix is ill-conditioned.

This error means one of two things is wrong with your .par file (located in each run of each subject’s bold directory): 1) there are not two or more occurrences of one of your conditions; or 2) there is a pattern to your conditions (for example condition 3 always follows condition 4). You can avoid this error message for the sake of analysis by 1) replacing other conditions with occurrences of your missing condition, so that each condition is represented at least twice; or 2) by changing your conditions so that they break the pattern at least twice. Even though the effect of this change is quite small, you should distribute the added conditions evenly across the other conditions. Ideally, however, you would alter your stimuli so that you do not get this error in the first place.

On 12/09/2015 02:19 PM, Christina Pressl wrote: hi doug,

thank you so much for your quick reply. yes - I saw this error after I sent you the error log. I checked the paradigm file, corrected it and rerun everything.

now this error is gone but I still get the following:

Error using svd Input to SVD must not contain NaN or Inf. Error in cond (line 36) s = svd(A);

Error in fast_selxavg3 (line254) XCond = cond(XtX);

- - - - - — - - — - - — - — -

EROOR: fast_selxavg3() failed\n

Your help is much appreciated

On Dec 9, 2015, at 1:57 PM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

Did you see the error description:

ERROR: /space/mdeh5/1/halgdev/projects/christina/FSFAST/Project/NC211_fmri_060515/Sess01/bold/004/oddeven.par is not correctly formatted. Line 19 only has 0 items

did you check this file?

On 12/09/2015 12:38 PM, Christina Pressl wrote: Dear Freesurfer Experts,

I am having trouble with selxavg3-sess and was wondering if you could maybe help me resolving the issue (error log attached)

I ran

#preproc-sess –s Sess01 –surface fsaverage lhrh –mni305 –fwhm 5 –per-run

and the following commands for lh, rh and mni305

#mkanalysis-sess –fsd bold –stc up -surface fsaverage lh -fwhm 5 -event-related -paradigm oddeven.par -nconditions 3 -spmhrf 0 -TR 2 -refeventdur 10.750 -nskip 4 –mcextreg -polyfit 2 -analysis oddeven.sm5.lh

#mkcontrast-sess –analysis oddeven.sm5.lh –contrast face-vs-object –a 1 –c 2 –c 3

#mkcontrast-sess –analysis oddeven.sm5.lh –contrast face-vs-fix –a 1 –c 0

Thank you very much.

Christina

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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto: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:https://gate.nmr.mgh.harvard.edu/filedrop2http://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/http://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto: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: https://gate.nmr.mgh.harvard.edu/filedrop2 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/

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