Hi Joshua, you do not have samples for all of your groups (eg, group0bp2-2-1). doug
On 04/04/2013 11:59 PM, Joshua deSouza wrote: > Hello Douglas, > > I have done as you have suggested and have created 16 classes with 2 > different groups, and 3 discreet variables. However, I seem to be > getting the same error but with a a different condo. The error is : > matrix is ill-conditioned or bad scaled, condo = 1e+08. The only 2 > continous variables are age and TIV. There is no strong correlation > between either continous variable. I also used another group instead > because the sample size was larger and I thought it might help. > > The FSGD file = thomas6.txt > The design matrix = Xg.dat > The contrast matrix = t6.txt > > Please let me know on what should be done or if I have overlooked > anything. I have done the necessary processing according to the steps > in the tutorial. Please let me know if you require any morer files > such as the .mgh files. > > Thank you for your time in this matter. > Joshua > > > On Thu, Apr 4, 2013 at 11:47 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > Hi Joshua, you should start by not coding gender and handedness as > continuous variables. In doing this, you are saying that you expect > right handers to have 2x the thickness as left handers (or females to > have 2x the thickness as males). You need 8 classes. If your "voxel" > variable is discrete, then you will need 16 classes. > doug > > > > > On 04/04/2013 05:22 AM, Joshua deSouza wrote: > > > > Hello Sir/Madam, > > > > I am currently running a statistical test using the FSGD method. > I am > > encountering a problem in relation to the creation of the glmdir > > folder when I run the mri_glmfit function. I recieve an ERROR > message > > that tells me that the design matrix (automatically generated) > is ill > > conditioned or badly scaled, condo = 10565.7. All the steps before > > creating the glmdir folder have been done in accordance with the > FSGD > > group analysis tutorial on the freesurfer wiki. > > > > The command line is : mri_glmfit --y lh.thomas4.10.mgh --fsgd > > thomas4.txt dods --C t4.txt --surf fsaverage lh --cortex --glmdir > > lh.thomas4.glmdir > > > > The FSGD file = thomas4.txt ( contains 2 groups and 5 variables) > > The data matrix = Xg.dat > > The contrast matrix = t4.txt > > > > There are 3 columns of variables that have discreet values of > either 1 > > or 2. However I have tried this with another FSGD file (thomas3.txt) > > that contained 4 variables of which 2 were continous and the > other 2 > > were in 1s' and 2s'. > > > > The contrast matrix of thomas3.txt = C.dat > > The design matrix of thomas3.txt = Xg1.dat > > > > I was able to generate a glmdir using mri_glmfit with > thomas3.txt and > > generate a surface for tksurfer to use. The file created was the > > sig.mgh file which was then compared with the fsaverage files. > However > > once I added another variable titled "voxel" in thomas4.txt, I > > received the error message. > > > > I did a correlation of the columns containing 1s and 2s in the FSGD > > file thomas4.txt using Matlab and have not found any significant > > correlation with each other. > > > > Please do advise on how to solve this issue and also from where the > > problem could stem from as I am unsure as to the nature of the > problem. > > > > Thank You for your patience and assistance > > > > Joshua > > > > > > > > _______________________________________________ > > 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 > gr...@nmr.mgh.harvard.edu <mailto:gr...@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> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
