Can you send the Xg.dat file?
On 7/3/2019 2:44 PM, Marie Hill wrote:
External Email - Use Caution
Command line: mri_glmfit --y lh.g4v1.10.mgh --fsgd g4v1.fsgd dods --C
healthy-vs-bipolar-and-schizophrenia.mtx --C healthy-vs-bipolar.mtx --C
healthy-vs-schizophrenia.mtx --C bipolar-vs-schizophrenia.mtx --C
none-vs-risk-allele.mtx --surf fsaverage lh --cortex --glmdir lh.g4v1.glmdir
Full terminal output:
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 6.97972e-07 0.988303
Class Means of each Continuous Variable
1 h_n_f 0.3741
2 h_r_f -0.6420
3 h_n_m -0.8145
4 h_r_m -0.3544
5 b_n_f -0.9296
6 b_r_f -0.7187
7 b_n_m 0.7958
8 b_r_m 0.3549
9 s_n_f 0.4364
10 s_r_f 0.4124
11 s_n_m 0.0769
12 s_r_m -0.6899
INFO: gd2mtx_method is dods
Reading source surface /home/k1895485/scans/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces 327680
Total area 65416.984375
AvgVtxArea 0.399269
AvgVtxDist 0.721953
StdVtxDist 0.195470
$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
cwd /home/k1895485/scans
cmdline mri_glmfit.bin --y lh.g4v1.10.mgh --fsgd g4v1.fsgd dods --C
healthy-vs-bipolar-and-schizophrenia.mtx --C healthy-vs-bipolar.mtx --C
healthy-vs-schizophrenia.mtx --C bipolar-vs-schizophrenia.mtx --C
none-vs-risk-allele.mtx --surf fsaverage lh --cortex --glmdir lh.g4v1.glmdir
sysname Linux
hostname login1.nan.kcl.ac.uk
machine x86_64
user k1895485
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y /home/k1895485/scans/lh.g4v1.10.mgh
logyflag 0
usedti 0
FSGD g4v1.fsgd
labelmask /home/k1895485/scans/fsaverage/label/lh.cortex.label
maskinv 0
glmdir lh.g4v1.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory lh.g4v1.glmdir
Loading y from /home/k1895485/scans/lh.g4v1.10.mgh
... done reading.
INFO: gd2mtx_method is dods
Saving design matrix to lh.g4v1.glmdir/Xg.dat
Computing normalized matrix
Normalized matrix condition is 1e+08
Design matrix ------------------
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--------------------------------
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.bin --y lh.g4v1.10.mgh --fsgd g4v1.fsgd dods --C
healthy-vs-bipolar-and-schizophrenia.mtx --C healthy-vs-bipolar.mtx --C
healthy-vs-schizophrenia.mtx --C bipolar-vs-schizophrenia.mtx --C
none-vs-risk-allele.mtx --surf fsaverage lh --cortex --glmdir lh.g4v1.glmdir
2. The FSGD file (if using one)
3. And the design matrix above
Attempting to diagnose further
SumSq: Min=0.354440 (col 16), Max=2.741043 (col 19)
... could not determine the cause of the problem
Kind Regards,
Marie
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Greve, Douglas N.,Ph.D.
<dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
Sent: 03 July 2019 16:22
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Qdec Message to Mailing List
can you send the command line, full terminal output, your fsgd file, and the
Xg.dat created in the output?
On 7/3/2019 11:05 AM, Marie Hill wrote:
External Email - Use Caution
Thanks. When I run mri-glmfit I get Error: matrix is ill-conditioned or badly
scaled.
I have normalised the continuous variable Age.
Kind regards,
Marie
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Greve, Douglas N.,Ph.D.
<dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
Sent: 03 July 2019 15:24
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Qdec Message to Mailing List
yes, qdec can only have 2 factors with 2 levels. both qdec and mri_glmfit are
linear methods (in fact, qdec just calls mri_glmfit).
On 7/3/2019 9:39 AM, Marie Hill wrote:
External Email - Use Caution
Dear Sir/Madam,
Could I post the following message to the mailing list:
I am running a regression testing for significant difference in cortical
volume, thickness etc with 3 factors: diagnosis, genotype and gender, with age
as a nuisance factor.
I am using qdec but receiving Error: factor 2 must have 2 levels.
Is it true that Qdec only supports factors with 2 levels? There is a page for
qdec levels stating to create a file diagnosis.levels and state the three
levels. I did this however the same error occurs.
I was going to use glm_fit instead but I think my study isn't a linear
regression so isn't suitable (as I am not interested in the change with age,
just between groups).
Kind regards,
Marie
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
