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 faces 327680

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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