Hi Doug,
Can I do this by just permuting the contrast matrix and the
corresponding columns
in the fsgd file?
Ed
On 26 Feb 2013, at 17:43, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
Hi Ed, I think it is just the way you have the matrix set up. You'll
need to alter the matrix in some way.
doug
Message: 7
Date: Tue, 26 Feb 2013 10:08:07 +0100
From: Ed Gronenschild <ed.gronensch...@maastrichtuniversity.nl>
Subject: Re: [Freesurfer] Problem with glmfit: matrix is
ill-conditioned
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<2031202f-e366-48cb-82a9-3142378ad...@maastrichtuniversity.nl>
Content-Type: text/plain; charset="us-ascii"
Hi Doug,
The condition numbers were:
- 1e+08 for problematic fsgd file
- 371.233 for previous fsgd file
I tried also v5.1, however with no succes. The matirx was still
ill-conditioned with condition number 2.80809e+07.
Cheers,
Ed
On 1 Feb 2013, at 9:53, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
Message: 12
Date: Thu, 31 Jan 2013 14:08:11 -0500
From: Douglas N Greve <gr...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Problem with glmfit: matrix is
ill-conditioned
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <510ac11b.4090...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Ed, that sounds strange. What were the condition numbers for the
two
analyses? This should be printed out into the terminal. It is also
possible that it is a scaling issue. This should not be an issue in
5.1,
but it is possible that it could have an effect if two columns are
very
similar.
doug
On 01/30/2013 05:10 AM, Ed Gronenschild wrote:
Hi Doug,
It is indeed correct that columns 1 and 17 are highly correlated.
However,
for another version of the fsgd file, where the corresponding
class and
covariate values where identical but with other covariates (so
leading to
the same columns 1 and 17, other columns are different), all went
well.
So probably some other columns are highly correlated as well.
Anyway, what can we do about it? Just leave the offending covariate
(s)
out?
Cheers,
Ed
Message: 1
Date: Thu, 24 Jan 2013 12:51:23 -0500
From: Douglas N Greve <gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Problem with glmfit: matrix is
ill-conditioned
To: freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
Message-ID: <5101749b.4060...@nmr.mgh.harvard.edu
<mailto:5101749b.4060...@nmr.mgh.harvard.edu>>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Ed, the problem is that your covariates are highly correlated.
Eg,
column 1 is nearly identical to column 17.
doug
On 01/24/2013 06:36 AM, Ed Gronenschild wrote:
Hi,
Running mri_glmfit ( v5.0.0, Mac OSX10.6) I got he following
error message:
ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
1. Your command line:
mri_glmfit --y lh.sib_con_cann_aangepast3.thickness.sm0.mgh
--fsgd
../../STATS/FSGD/age_gender_scan_educ_hand_cannabis/
fsgd_sib_con_cann_aangepast3.fsgd
dods --glmdir lh.sib_con_cann_aangepast3.dods.sm0.glmdir --surf
fsaverage lh --C
../../STATS/FSGD/age_gender_scan_educ_hand_cannabis/
group_thickness_gender_scan_age_educ_hand_cann.mtx
2. The FSGD file (if using one)
3. And the design matrix above
Please find attached the requested files.
I noticed that rows 68 and 147 of the matrix Xg.dat are identical,
and most probably caused the error.
In the fsgd file I see that the correspondig cases indeed have
identical values, although they are referring to different data.
How to proceed?
Cheers,
Ed
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MGH-NMR Center
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