It looks like you have created your fsgd file using a windows computer.
Try running
cat file.fsgd | sed 's/\\r/\\n/g' > new.file.fsgd
probably have to do the same with the contrast matrix file
On 11/9/15 9:18 PM, Gay,Charles Wysaw wrote:
Hi Freesurfer group -
I am receiving errors each time I try to run mri_glmfit. It appears to
be the way I set up either the fsgd or mtx file. Any assistance would
be greatly appreciated.
Thanks,
Chaz
Hypothesis for the contrast in the mtx file: Is there an average
affect of heat threshold regressing out the effect of gender and age?
Command-line executed:
mri_glmfit \--y lh.heatthreshold.thickness.10.mgh \--fsgd
heatthreshold.fsgd dods \--C g1g2.heatthreshold.age.mtx \--surf
fsaverage lh \--cortex \--glmdir lh.gender.heatthreshold.age.glmdir
I seem to be getting 1 or 2 errors
1: gdfReadHeader: reading heatthreshold1.fsgd
INFO: ignoring tag B113v1
INFO: ignoring tag B036V1
INFO: ignoring tag B015v1
INFO: ignoring tag B006v1
WARNING: gdfReadV1: class Male is defined but not used.
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 HeatThreshold nan nan
1 Age nan nan
Class Means of each Continuous Variable
1 Male nan nan
2 Female nan nan
INFO: gd2mtx_method is dods
Reading source surface
/Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/subjects/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces327680
Total area 65416.648438
AvgVtxArea 0.399267
AvgVtxDist 0.721953
StdVtxDist 0.195470
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd
/Volumes/projects/painimaging/Bishop/Abstracts/APS_2016/Correlation_Cortical_Thickness_Pain
Sensitivity/FSGDs/heat_threshold
cmdline mri_glmfit --y lh.heatthreshold.thickness.10.mgh --fsgd
heatthreshold1.fsgd dods --C g1g2.heatthreshold.age.mtx --surf
fsaverage lh --cortex --glmdir lh.gender.heatthreshold.age.glmdir
sysname Darwin
hostname phhp-chazgay-mb.ad.ufl.edu
machine x86_64
user chaz.gay
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y
/Volumes/projects/painimaging/Bishop/Abstracts/APS_2016/Correlation_Cortical_Thickness_Pain
Sensitivity/FSGDs/heat_threshold/lh.heatthreshold.thickness.10.mgh
logyflag 0
usedti 0
FSGD heatthreshold1.fsgd
labelmask
/Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/subjects/fsaverage/label/lh.cortex.label
maskinv 0
glmdir lh.gender.heatthreshold.age.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory lh.gender.heatthreshold.age.glmdir
Loading y from
/Volumes/projects/painimaging/Bishop/Abstracts/APS_2016/Correlation_Cortical_Thickness_Pain
Sensitivity/FSGDs/heat_threshold/lh.heatthreshold.thickness.10.mgh
INFO: gd2mtx_method is dods
Saving design matrix to lh.gender.heatthreshold.age.glmdir/Xg.dat
Normalized matrix condition is 1e+08
Design matrix --
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.heatthreshold.thickness.10.mgh --fsgd
heatthreshold1.fsgd dods --C g1g2.heatthreshold.age.mtx --surf
fsaverage lh --cortex --glmdir lh.gender.heatthreshold.age.glmdir
2. The FSGD file (if using one)
3. And the design matrix above
And 2
gdfReadHeader: reading heatthreshold.fsgd
ERROR: gdfReadV1: Input line 1, subjid = B113v1
Found 242 variables, expected. 2
FSGDF Format Error: file = heatthreshold.fsgd, tag=Input
I attached both the .mxt and fsgd files
Thanks again,
Chaz
FREESURFER_HOME:
/Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer
Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
Kernel info: Darwin 14.5.0 x86_64
-
Please include the following additional information in your report:
1) subject name
2) the entire command-line executed
3) the error message generated
4) optionally include the subject's /script/recon-all.log
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