External Email - Use Caution Hello,
Any idea how to solve this problem? I have tried the suggested solutions on the archive, that's Demean and Rescale but to no avail. I have attached the necessary files in the email below. Many thanks, Miracle mri_glmfit command: mri_glmfit --y results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.thickness.10B.mgh --fsgd thickness_DHI_Emotional_edit.fsgd dods --C thickness_edit.mtx --surf fsaverage lh --cortex --glmdir results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.glmdir
bash-3.2$ mri_glmfit --y
results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.thickness.10B.mgh
--fsgd thickness_DHI_Emotional_edit.fsgd dods --C thickness_edit.mtx --surf
fsaverage lh --cortex --glmdir
results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.glmdir
gdfRead(): reading thickness_DHI_Emotional_edit.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 47.0476 9.22459
1 Sports 0.619048 1.13289
2 Days_TBI 1734.1 919.571
3 Emotional 13.5238 7.19536
Class Size and Means of each Continuous Variable
1 PPCS_male 5 39.8000 1.6000 1557.8000 12.8000
2 PPCS_female 16 49.3125 0.3125 1789.1875 13.7500
WARNING: Class PPCS_male has 5 members. With 4 variables and using DODS, This
is the bare minimum which may cause problems with the design matrix.
INFO: gd2mtx_method is dods
Reading source surface
/Users/sergiolab/Documents/Miracle/Analysis/Cortical_thickness/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces 327680
Total area 65417.000000
AvgVtxArea 0.399269
AvgVtxDist 0.721953
StdVtxDist 0.195472
7.2.0
cwd /Users/sergiolab/Documents/Miracle/Analysis/Cortical_thickness
cmdline mri_glmfit --y
results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.thickness.10B.mgh
--fsgd thickness_DHI_Emotional_edit.fsgd dods --C thickness_edit.mtx --surf
fsaverage lh --cortex --glmdir
results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.glmdir
sysname Darwin
hostname ip-130-63-40-126.dynamic.yorku.ca
machine x86_64
user sergiolab
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y
/Users/sergiolab/Documents/Miracle/Analysis/Cortical_thickness/results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.thickness.10B.mgh
logyflag 0
usedti 0
FSGD thickness_DHI_Emotional_edit.fsgd
labelmask
/Users/sergiolab/Documents/Miracle/Analysis/Cortical_thickness/fsaverage/label/lh.cortex.label
maskinv 0
glmdir results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory
results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.glmdir
Loading y from
/Users/sergiolab/Documents/Miracle/Analysis/Cortical_thickness/results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.thickness.10B.mgh
... done reading.
INFO: gd2mtx_method is dods
Saving design matrix to
results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.glmdir/Xg.dat
Computing normalized matrix
Normalized matrix condition is 653034
Design matrix ------------------
1.00000 0.00000 30.00000 0.00000 4.00000 0.00000 1687.00000
0.00000 10.00000 0.00000;
0.00000 1.00000 0.00000 46.00000 0.00000 0.00000 0.00000
2149.00000 0.00000 12.00000;
1.00000 0.00000 41.00000 0.00000 0.00000 0.00000 2148.00000
0.00000 6.00000 0.00000;
0.00000 1.00000 0.00000 49.00000 0.00000 0.00000 0.00000
2257.00000 0.00000 18.00000;
0.00000 1.00000 0.00000 51.00000 0.00000 0.00000 0.00000
1939.00000 0.00000 28.00000;
0.00000 1.00000 0.00000 61.00000 0.00000 0.00000 0.00000
3404.00000 0.00000 8.00000;
0.00000 1.00000 0.00000 53.00000 0.00000 0.00000 0.00000
2368.95825 0.00000 6.00000;
0.00000 1.00000 0.00000 60.00000 0.00000 2.00000 0.00000
1407.00000 0.00000 10.00000;
0.00000 1.00000 0.00000 48.00000 0.00000 0.00000 0.00000
1670.95837 0.00000 6.00000;
0.00000 1.00000 0.00000 38.00000 0.00000 0.00000 0.00000
12.00000 0.00000 26.00000;
0.00000 1.00000 0.00000 63.00000 0.00000 0.00000 0.00000
796.00000 0.00000 18.00000;
0.00000 1.00000 0.00000 40.00000 0.00000 0.00000 0.00000
476.00000 0.00000 6.00000;
0.00000 1.00000 0.00000 44.00000 0.00000 2.00000 0.00000
1980.00000 0.00000 14.00000;
0.00000 1.00000 0.00000 50.00000 0.00000 1.00000 0.00000
3517.04175 0.00000 6.00000;
1.00000 0.00000 29.00000 0.00000 1.00000 0.00000 177.04167
0.00000 18.00000 0.00000;
0.00000 1.00000 0.00000 39.00000 0.00000 0.00000 0.00000
2571.00000 0.00000 22.00000;
0.00000 1.00000 0.00000 53.00000 0.00000 0.00000 0.00000
1872.00000 0.00000 18.00000;
1.00000 0.00000 59.00000 0.00000 0.00000 0.00000 1148.00000
0.00000 24.00000 0.00000;
0.00000 1.00000 0.00000 50.00000 0.00000 0.00000 0.00000
1250.04163 0.00000 16.00000;
1.00000 0.00000 40.00000 0.00000 3.00000 0.00000 2628.95825
0.00000 6.00000 0.00000;
0.00000 1.00000 0.00000 44.00000 0.00000 0.00000 0.00000
957.00000 0.00000 6.00000;
--------------------------------
ERROR: matrix is ill-conditioned or badly scaled, condno = 653034
--------------------------------
-------- ERROR: READ THIS -----------------
--vvvvvvvvvvvvvvvvvvvvvvvvvvvvvv-----
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
results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.thickness.10B.mgh
--fsgd thickness_DHI_Emotional_edit.fsgd dods --C thickness_edit.mtx --surf
fsaverage lh --cortex --glmdir
results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.glmdir
2. The terminal output of this program (ie, everything it prints to the
screen)
3. The FSGD file (thickness_DHI_Emotional_edit.fsgd)
4. The design matrix
results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.glmdir/Xg.dat
Attempting to diagnose further
WARNING: Class PPCS_male has 5 members. With 4 variables and using DODS, This
is the bare minimum which may cause problems with the design matrix.
SumSq: Min=2.236068 (col 1), Max=8073.791016 (col 8)
The scale is much different between columns 1 and 8, you may want to
normalize by subtracting the mean and dividing by the standard deviation.
--^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^----
bash-3.2$
Xg.dat
Description: Binary data
thickness_DHI_Emotional_edit.fsgd
Description: Binary data
_______________________________________________ Freesurfer mailing list 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
