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 <greve@nmr.mgh.harvard.edu mailto:greve@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
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>
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.