You have a table of data, so no template is needed. If you put the --surf before the --table, it probably runs, but it will ignore the surface
On 4/18/17 9:58 PM, miracooloz@gmail.com wrote:
Thanks doug. Does it mean when using the --table flag, you can't use the fsaverage template? I came across several post in the forum that used "--surf fsaverage lh " and it worked.Best,Paul
Sent from my BlackBerry 10smartphone.
Don't include --surf fsaverage lh. It thinks the input is a surface, not a table
On 4/18/17 9:21 PM, miracle ozzoude wrote:
Hello freesurfer,I am trying to run mri_glmfit with the --table flag. My aparc_lh_thick_stats.txt contain entorhinal and parahippocampal thickness values for 32 subjects. I ran the glm command and received an error. Please, how can i solve this issue? I have included my command, fsgd file, contrast matrix and error below. ThanksBest,Paul
GLM command: mri_glmfit --table aparc_lh_thick_stats.txt --fsgd age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex --glmdir lh.thickness.glmdir
ERROR= "gdfRead(): reading age.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 39.9375 17.3312
Class Means of each Continuous Variable
1 Group1 35.6316
2 Group2 46.2308
INFO: gd2mtx_method is dods
Reading source surface /Users/MiracleOz/Documents/
improvervsdeclinermri/ 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 /Users/MiracleOz/Documents/
improvervsdeclinermri cmdline mri_glmfit.bin --table aparc_lh_thick_stats.txt --fsgd age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex --glmdir lh.thickness.glmdir
sysname Darwin
hostname MacBook-Pro.local
machine x86_64
user MiracleOz
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y /Users/MiracleOz/Documents/
improvervsdeclinermri/aparc_ lh_thick_stats.txt logyflag 0
usedti 0
FSGD age.fsgd
labelmask /Users/MiracleOz/Documents/
improvervsdeclinermri/ fsaverage/label/lh.cortex. label maskinv 0
glmdir lh.thickness.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory lh.thickness.glmdir
Loading y from /Users/MiracleOz/Documents/
improvervsdeclinermri/aparc_ lh_thick_stats.txt Found 66 data colums
Found 0 data rows
INFO: gd2mtx_method is dods
Saving design matrix to lh.thickness.glmdir/Xg.dat
Computing normalized matrix
Normalized matrix condition is 32.2165
Matrix condition is 20734.7
Found 149955 points in label.
ERROR: mri_reshape: number of elements cannot change
nv1 = 163842, nv1 = 66
search space = 82219.962936
ERROR: dimension mismatch between y and X.
y has 0 inputs, X has 32 rows."
FSGD file: GroupDescriptorFile 1
Title MOT
Class Group1
Class Group2
Variables Age
Input 01053p Group1 23
Input 01054p Group1 43
Input 01061p Group2 39
Input 01062p Group2 19
Input 01074p Group2 28
.............. (I have more participants)
CONTRAST MATRIX: 1 -1 0 0
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