I added normalizing and demeaning code like you suggested in my fsgd file and perform the GLM analysis (mri_glmfit). However, my covariates were only demeaned (DeMeanFlag 1) but they were not normalized (ReScaleFlag 1). Hence I received this error from freesurfer. I have attached my fsgd files and contrast matrix INFO: demeaning continuous variables Continuous Variable Means (all subjects) 0 Age 39.9375 17.3312 1 Education 15.5625 1.99902 2 Firstscore 1.03375 0.341785 3 Secondscore 1.03906 0.370678 4 Thirdscore 1.13844 0.4768 5 Averagescore 1.07375 0.364046 Class Means of each Continuous Variable 1 Group1 35.6316 15.0526 1.0342 1.2111 1.4289 1.2305 2 Group2 46.2308 16.3077 1.0331 0.7877 0.7138 0.8446 INFO: gd2mtx_method is dods Reading source surface /Users/ctartaglia/Desktop/improvervsdeclinermri/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470
$Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $
cwd /Users/ctartaglia/Desktop/improvervsdeclinermri
cmdline mri_glmfit --y lh.NeuroTrackerscore.thickness.10B.mgh --fsgd
NeuroTrackerscore.fsgd dods --C new.firstmatrix.mtx --C
new.secondmatrix.mtx --C new.thirdmatrix.mtx --C new.fourthmatrix.mtx --C
new.fifthmatrix.mtx --C new.sixthmatrix.mtx --C new.seventhmatrix.mtx --C
new.eightmatrix.mtx --C new.ninethmatrix.mtx --C new.tenthmatrix.mtx --surf
fsaverage lh --cortex --glmdir lh.NeuroTrackerscore.glmdir
sysname Darwin
hostname twh-ct-lab4-imac.uhn.ca
machine x86_64
user ctartaglia
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y
/Users/ctartaglia/Desktop/improvervsdeclinermri/lh.NeuroTrackerscore.thickness.10B.mgh
logyflag 0
usedti 0
FSGD NeuroTrackerscore.fsgd
labelmask
/Users/ctartaglia/Desktop/improvervsdeclinermri/fsaverage/label/lh.cortex.label
maskinv 0
glmdir lh.NeuroTrackerscore.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory lh.NeuroTrackerscore.glmdir
Loading y from
/Users/ctartaglia/Desktop/improvervsdeclinermri/lh.NeuroTrackerscore.thickness.10B.mgh
INFO: gd2mtx_method is dods
Saving design matrix to lh.NeuroTrackerscore.glmdir/Xg.dat
Normalized matrix condition is 115605
Design matrix ------------------
1.000 0.000 -0.729 0.000 -0.026 0.000 1.889 0.000 1.535
0.000 1.428 0.000 1.729 0.000;
1.000 0.000 0.425 0.000 0.474 0.000 -0.568 0.000 -0.866
0.000 -0.501 0.000 -0.716 0.000;
1.000 0.000 0.194 0.000 0.974 0.000 -0.715 0.000 -1.001
0.000 -0.438 0.000 -0.771 0.000;
1.000 0.000 -0.960 0.000 -1.027 0.000 -0.568 0.000 -0.408
0.000 -0.354 0.000 -0.496 0.000;
1.000 0.000 -0.440 0.000 -1.027 0.000 0.075 0.000 -0.246
0.000 -0.124 0.000 -0.139 0.000;
1.000 0.000 -0.440 0.000 1.474 0.000 -0.188 0.000 0.132
0.000 -0.208 0.000 -0.111 0.000;
1.000 0.000 0.079 0.000 0.474 0.000 -0.480 0.000 -0.165
0.000 -0.124 0.000 -0.276 0.000;
1.000 0.000 -0.902 0.000 -0.527 0.000 -0.100 0.000 0.429
0.000 0.044 0.000 0.108 0.000;
1.000 0.000 1.291 0.000 0.474 0.000 -0.188 0.000 -0.246
0.000 -0.040 0.000 0.108 0.000;
1.000 0.000 -0.440 0.000 1.474 0.000 -0.480 0.000 -0.569
0.000 -0.900 0.000 -0.743 0.000;
1.000 0.000 0.598 0.000 0.474 0.000 -0.773 0.000 -0.408
0.000 0.317 0.000 -0.249 0.000;
1.000 0.000 -0.844 0.000 0.474 0.000 1.597 0.000 1.535
0.000 0.736 0.000 1.317 0.000;
1.000 0.000 -0.787 0.000 0.474 0.000 1.363 0.000 0.024
0.000 0.422 0.000 0.603 0.000;
1.000 0.000 -0.960 0.000 -1.027 0.000 1.480 0.000 1.265
0.000 1.428 0.000 1.509 0.000;
1.000 0.000 -1.075 0.000 -1.527 0.000 -0.100 0.000 -0.327
0.000 -0.270 0.000 -0.276 0.000;
1.000 0.000 0.887 0.000 0.474 0.000 -0.276 0.000 0.887
0.000 0.527 0.000 0.438 0.000;
1.000 0.000 0.483 0.000 0.474 0.000 0.544 0.000 0.240
0.000 0.149 0.000 0.301 0.000;
1.000 0.000 2.445 0.000 -1.527 0.000 -1.241 0.000 -0.246
0.000 -0.585 0.000 -0.743 0.000;
1.000 0.000 1.175 0.000 -1.027 0.000 -1.270 0.000 -1.568
0.000 -1.508 0.000 -1.595 0.000;
0.000 1.000 0.000 0.217 0.000 0.847 0.000 0.254 0.000
0.411 0.000 0.474 0.000 0.427;
0.000 1.000 0.000 -1.513 0.000 -0.654 0.000 0.254 0.000
0.141 0.000 -0.239 0.000 0.015;
0.000 1.000 0.000 0.102 0.000 -0.154 0.000 -1.764 0.000
-1.181 0.000 -0.763 0.000 -1.276;
0.000 1.000 0.000 -1.340 0.000 -0.154 0.000 1.600 0.000
1.166 0.000 1.062 0.000 1.361;
0.000 1.000 0.000 -1.687 0.000 0.346 0.000 1.366 0.000
1.274 0.000 0.999 0.000 1.306;
0.000 1.000 0.000 0.275 0.000 0.847 0.000 -0.828 0.000
-0.264 0.000 -0.239 0.000 -0.452;
0.000 1.000 0.000 -0.186 0.000 0.847 0.000 0.869 0.000
0.276 0.000 0.328 0.000 0.509;
0.000 1.000 0.000 0.737 0.000 -0.154 0.000 -0.623 0.000
-0.506 0.000 -0.239 0.000 -0.480;
0.000 1.000 0.000 -0.013 0.000 1.347 0.000 -0.623 0.000
0.006 0.000 -0.008 0.000 -0.205;
0.000 1.000 0.000 1.025 0.000 -1.655 0.000 -0.331 0.000
-0.641 0.000 -0.532 0.000 -0.562;
0.000 1.000 0.000 0.160 0.000 -0.154 0.000 1.600 0.000
0.654 0.000 0.369 0.000 0.894;
0.000 1.000 0.000 1.833 0.000 -2.155 0.000 -1.852 0.000
-1.828 0.000 -1.287 0.000 -1.771;
0.000 1.000 0.000 0.391 0.000 0.847 0.000 0.079 0.000
0.492 0.000 0.076 0.000 0.235;
--------------------------------
ERROR: matrix is ill-conditioned or badly scaled, condno = 115605
--------------------------------
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.NeuroTrackerscore.thickness.10B.mgh --fsgd
NeuroTrackerscore.fsgd dods --C new.firstmatrix.mtx --C
new.secondmatrix.mtx --C new.thirdmatrix.mtx --C new.fourthmatrix.mtx --C
new.fifthmatrix.mtx --C new.sixthmatrix.mtx --C new.seventhmatrix.mtx --C
new.eightmatrix.mtx --C new.ninethmatrix.mtx --C new.tenthmatrix.mtx --surf
fsaverage lh --cortex --glmdir lh.NeuroTrackerscore.glmdir
2. The FSGD file (if using one)
3. And the design matrix above
On Tue, Jul 26, 2016 at 12:23 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu
> wrote:
> what do you mean it did not work? can you be more specific?
>
>
> On 07/26/2016 12:21 PM, miracle ozzoude wrote:
> > Hello Doug,
> > The ReScaleFlag 1 command did not work. Only the demean command.
> > Paul
> >
> >
> > On Mon, Jul 25, 2016 at 6:17 PM, Douglas Greve
> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > Actually, I checked the code and found that I had already put a
> > flag in there to do this (I'm so clever). Add
> >
> > ReScaleFlag 1
> >
> > in addition to
> >
> > DeMeanFlag 1
> >
> >
> >
> >
> > On 7/25/16 11:22 AM, Douglas Greve wrote:
> >>
> >> No, that flag does not exist, but it is a good idea! You'll have
> >> to normalize them by hand.
> >>
> >>
> >> On 7/24/16 1:33 PM, miracle ozzoude wrote:
> >>> Hello freesurfer experts,
> >>> I am trying to normalize my continuous variables in my fsgd
> >>> file. Is this the correct term to add to my fsgd file in order
> >>> for mri_glmfit to normalize it?
> >>>
> >>> GroupDescriptorFile 1
> >>> Title PCS
> >>> Class group1
> >>> Class group2
> >>> Normalize 1
> >>> Variables Age Education Scoreone Scoretwo
> >>> Input 053 group1 47 18 3.4 5.6
> >>> Input 054 group2 50 16 5.3 2.8
> >>>
> >>> Thank you,
> >>> Paul
> >>>
> >>>
> >>> _______________________________________________
> >>> 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
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> 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
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> > but does not contain patient information, please contact the
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> >
> >
> >
> >
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>
> --
> 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
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NeuroTrackerscore.fsgd
Description: Binary data
new.eightmatrix.mtx
Description: Binary data
new.fifthmatrix.mtx
Description: Binary data
new.firstmatrix.mtx
Description: Binary data
new.fourthmatrix.mtx
Description: Binary data
new.ninethmatrix.mtx
Description: Binary data
new.secondmatrix.mtx
Description: Binary data
new.seventhmatrix.mtx
Description: Binary data
new.sixthmatrix.mtx
Description: Binary data
new.tenthmatrix.mtx
Description: Binary data
new.thirdmatrix.mtx
Description: Binary data
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