[Freesurfer] Matrix is singluar to working precision
Hi Freesurfers,
I'm trying to selxavg3 my data.
My design includes 6 conditions including a 0 rest condition. 3 contrasts
have been defined using mkcontrast. The analysis too using mkanalysis.
I use this command line :
[/homes/11/chaumon/data] (nmr-std-env) selxavg3-sess -analysis
"Analyse_Simple_Confidence" -s S003 -overwrite
Which returns what's in the log file attached.
and ends with
Creating Design Matrix
Warning: Matrix is singular to working precision.
> In fast_selxavg3 at 212
Warning: Matrix is singular to working precision.
> In fast_selxavg3 at 212
Warning: Matrix is singular to working precision.
> In fast_selxavg3 at 212
Warning: Matrix is singular to working precision.
> In fast_selxavg3 at 212
Warning: Matrix is singular to working precision.
> In fast_selxavg3 at 212
Warning: Matrix is singular to working precision.
> In fast_selxavg3 at 212
Warning: Matrix is singular to working precision.
> In fast_selxavg3 at 212
Warning: Matrix is singular to working precision.
> In fast_selxavg3 at 212
Warning: Matrix is singular to working precision.
> In fast_selxavg3 at 212
ntptot = 693, nX = 15, DOF = 678
Saving X matrix to
/autofs/space/bomba_016/users/chaumon/S003/bold/Analyse_Simple_Confidence/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 248
XCond = cond(XtX);
>> 09-Oct-2009 18:03:13
Salut !
--
ERROR: fast_selxavg3() failed\n
I'm puzzled. I've been checking and rechecking my design. The problem does
not come from the contrasts because I get the same error if I remove them...
Any help will be greatly appreciated.
Thanks,
Max
selxavg3-sess log file
/usr/local/freesurfer/stable4/fsfast/bin/selxavg3-sess
-analysis Analyse_Simple_Confidence -s S003 -overwrite
$Id: selxavg3-sess,v 1.32.2.5 2009/04/17 20:09:46 greve Exp $
uid=7466(chaumon) gid=7466(chaumon) groups=1066(bargp),1134(barw1gp),3002(acqmbar),7466(chaumon)
/autofs/space/bomba_016/users/chaumon
Linux labutokail 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 09:10:25 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
Fri Oct 9 18:03:08 EDT 2009
---
/autofs/space/bomba_016/users/chaumon/S003
Fri Oct 9 18:03:08 EDT 2009
anadir = /autofs/space/bomba_016/users/chaumon/S003/bold/Analyse_Simple_Confidence
analysis Analyse_Simple_Confidence alread exists for S003
... reanalyzing (deleting old analysis)
--
% Fri Oct 9 18:03:08 EDT 2009
% /autofs/space/bomba_016/users/chaumon
% Analyse_Simple_Confidence
%
which fast_selxavg3
okfile = '/tmp/selxavg3-sess-554.ok';
if(fast_fileexists(okfile)) delete(okfile); end
monly = 0;
perrun = 0;
jkrun = 0;
DoGLMFit = 1;
DoContrasts= 1;
ConList= splitstring('');
DoSynth= 0;
UseFloat = 0;
SynthNoiseAmp = 1;
SynthNoiseAR1 = .3;
SynthSignalAmp = 0;
SynthSeed = -1;
sess = '/autofs/space/bomba_016/users/chaumon/S003';
analysis = 'Analyse_Simple_Confidence';
flacname = '';
outtop = '';
SaveResUnwhitened = 0;
fast_selxavg3;
if(~fast_fileexists(okfile) && ~monly); quit; end
quit;
--
--
--- matlab output
Warning: Unable to open display iconic, MATLAB is starting without a display.
You will not be able to display graphics on the screen.
< M A T L A B >
Copyright 1984-2007 The MathWorks, Inc.
Version 7.4.0.287 (R2007a)
January 29, 2007
Warning: Name is nonexistent or not a directory: /usr/pubsw/common/matlab/7.4/toolbox/matlab/randfun.
Warning: Name is nonexistent or not a directory: /usr/pubsw/common/matlab/7.4/toolbox/matlab/datamanager.
Warning: Name is nonexistent or not a directory: /usr/pubsw/common/matlab/7.4/toolbox/shared/dastudio/depviewer.
Warning: Name is nonexistent or not a directory: /usr/pubsw/common/matlab/7.4/toolbox/shared/sigbldr.
Warning: Name is nonexistent or not a directory: /usr/pubsw/common/matlab/7.4/toolbox/rtw/accel.
Warning: Name is nonexistent or not a directory: /usr/pubsw/common/matlab/7.4/toolbox/shared/simtargets.
Warning: Name is nonexistent or not a directory: /usr/pubsw/common/matlab/7.4/toolbox/fixedpoint/fixedpointtool.
Warning: Name is nonexistent or not a directory: /usr/pubsw/common/matlab/7.4/toolbox/images/colorspaces.
Warning: Name is nonexistent or not a directory: /usr/pubsw/common/matlab/7.4/toolbox/images/iptformats.
Warning: Name is nonexistent or not a directory: /usr/pubsw/common/matlab/7.4/toolbox/shared/siglib.
Warning: Name is nonexistent or not a directory: /usr/pubsw/common/matlab/7.4/toolbox/shared/sldv.
Warning: Name is nonexistent or not a directory: /usr/pubsw/common/matlab/7.4/toolbox/shared/statslib.
Warning: Name
Re: [Freesurfer] isxconcat-sess
Hi freesurfers, I've been running isxconcat-sess with this line chaumon[/homes/11/chaumon/data] (nmr-std-env) isxconcat-sess -sf subjlist.txt -analysis Analyse_Simple_Confidence -c High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor -o AVG08 I was expecting to find a directory called osgm in the specified analysis directory with which I could feed data to mri_glmfit, but I can't find it. /homes/11/chaumon/bomba/AVG08/Analyse_Simple_Confidence/High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor The log file is attached. I don't find "error" in the text. Where am I wrong? Is there any mri_glmfit-sess like script somewhere? It's going to be pretty tough to find each parameter to feed to mri_glmfit... Thanks, Max ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] isxconcat-sess
Thanks Doug, I was just a bit confused because I thought the help for mri_glmfit mentioned an osgm directory that wasn't there. I was given a matlab script that does that now. I'm using a command like this: mri_glmfit --y tal.ces.000.nii --osgm --glmdir tal.rfx.osgm --nii --mask ../tal.mask.nii Thanks Mx 2009/10/15 Doug Greve > > isxconcat-sess creates the files that you pass to mri_glmfit (ie, > multi-frame volumes and/or surfaces where each frame is a > subject). Something like: > > > AVG08/Analyse_Simple_Confidence/High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor/tal.ces.nii > > You can then use this as input to mri_glmfit passing it with > the --y option. You can get more help from the FS FAST tutorial. Go to > the wiki, type "isxconcat-sess" in the Search field, then hit the > "Text" button. > > doug > > > > On Wed, 14 Oct 2009, Maximilien Chaumon wrote: > > Hi freesurfers, >> >> I've been running isxconcat-sess with this line >> >> chaumon[/homes/11/chaumon/data] (nmr-std-env) isxconcat-sess -sf >> subjlist.txt -analysis Analyse_Simple_Confidence -c >> High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor -o AVG08 >> >> I was expecting to find a directory called osgm in the specified analysis >> directory with which I could feed data to mri_glmfit, but I can't find it. >> >> /homes/11/chaumon/bomba/AVG08/Analyse_Simple_Confidence/High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor >> >> The log file is attached. I don't find "error" in the text. >> >> Where am I wrong? >> Is there any mri_glmfit-sess like script somewhere? It's going to be >> pretty >> tough to find each parameter to feed to mri_glmfit... >> >> Thanks, >> Max >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FSfast - excluding time points from my analysis
Hi Freesurfers, I would like to be able to regress out specific time points from my functionals using FSfast. I thought I should do it with the -extreg option to mkanalysis-sess but I don't know how to create the required extregstem_000.bfloat file. How can I create this file? Thanks, Max ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FSfast - excluding time points from my analysis
Sent that earlier but seems like it didn't post. Sorry if it's a second posting. Hi Freesurfers, I would like to be able to regress out specific time points from my functionals using FSfast. I thought I should do it with the -extreg option to mkanalysis-sess but I don't know how to create the required extregstem_000.bfloat file. How can I create this file? Thanks, Max > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] design is ill-conditioned
Hi freesurfers, I'm trying to run an estimation with my last subject and get stuck with a ERROR: design is ill-conditioned I can imagine this means that my design misses something bu I can't find what. Conditions all have events in all runs, time points are equally spaced. Here's the log of the session /autofs/space/bomba_016/users/chaumon/log/selxavg3-sess-bold-Analyse_Simple_Confidence-091215135329.log Thanks for any help, Max ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] nmr-std-env error on seychelles
Hi Freesurfers,
I have an issue with a job I launch on seychelles.
I get this error message:
/usr/local/freesurfer/nmr-std-env: line 98: syntax error near unexpected
token `('
/usr/local/freesurfer/nmr-std-env: line 98: ` set path = ( /usr/pubsw/bin
$path )'
/var/spool/PBS/mom_priv/jobs/1258634.sey.SC: line 13: isxconcat-sess:
command not found
Since this is not a file I edited myself, I wonder what's wrong...
Thanks,
Max
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