Dear Experts,
I am running a rmanova using FSGD file and mri_glmfit.
I have done the mris_preproc step, and am currently trying to do the mri_glmfit step.
I keep getting an error that appears to be related to the contrast files and matricies (highlighted in yellow below)
I have also attched the FSGD file and a contrast file.
Everything is in ASCII.
The output from the command terminal is below:
mri_glmfit --glmdir lh.rmanova --y lh.thickness.mgh --fsgd rmanova.fsgd doss --C tp1_vs_tp2.mtx --C tp1_vs_tp3.mtx --C tp2_vs_tp3.mtx --C tp_effect.mtx --C mean.mtx --surface fsaverage lh
gdfReadHeader: reading rmanova.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 tp1_vs_tp2 0 0.840168
1 tp2_vs_tp3 0 0.766965
Class Means of each Continuous Variable
1 ECT_001 0.0000 0.0000
2 ECT_002 0.0000 0.0000
3 ECT_003 0.0000 0.0000
4 ECT_004 0.0000 0.0000
5 ECT_005 0.0000 0.0000
6 ECT_006 0.0000 0.0000
7 ECT_007 0.0000 0.0000
8 ECT_008 0.0000 0.0000
9 ECT_009 0.0000 0.0000
10 ECT_010 0.0000 0.0000
11 ECT_011 0.0000 0.0000
12 ECT_012 0.0000 0.0000
13 ECT_013 0.0000 0.0000
14 ECT_014 0.0000 0.0000
15 ECT_015 0.0000 0.0000
16 ECT_016 0.0000 0.0000
17 ECT_017 0.0000 0.0000
18 ECT_018 0.0000 0.0000
19 ECT_019 0.0000 0.0000
20 ECT_020 0.0000 0.0000
21 ECT_021 0.0000 0.0000
22 ECT_022 0.0000 0.0000
23 ECT_023 0.0000 0.0000
24 ECT_024 0.0000 0.0000
INFO: gd2mtx_method is doss
Reading source surface /media/My_Book/MyDATA/ECT_Structure_For_Harry/FreeSurfer_Analysis/priorEDIT/T1/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 /media/My_Book/MyDATA/ECT_Structure_For_Harry/FreeSurfer_Analysis/priorEDIT/T1
cmdline mri_glmfit --glmdir lh.rmanova --y lh.thickness.mgh --fsgd rmanova.fsgd doss --C tp1_vs_tp2.mtx --C tp1_vs_tp3.mtx --C tp2_vs_tp3.mtx --C tp_effect.mtx --C mean.mtx --surface fsaverage lh
sysname Linux
hostname fs-OptiPlex-755
machine i686
user fs
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y /media/My_Book/MyDATA/ECT_Structure_For_Harry/FreeSurfer_Analysis/priorEDIT/T1/lh.thickness.mgh
logyflag 0
usedti 0
FSGD rmanova.fsgd
labelmask /media/My_Book/MyDATA/ECT_Structure_For_Harry/FreeSurfer_Analysis/priorEDIT/T1/fsaverage/label/lh.cortex.label
maskinv 0
glmdir lh.rmanova
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory lh.rmanova
Loading y from /media/My_Book/MyDATA/ECT_Structure_For_Harry/FreeSurfer_Analysis/priorEDIT/T1/lh.thickness.mgh
INFO: gd2mtx_method is doss
Saving design matrix to lh.rmanova/Xg.dat
Normalized matrix condition is 2.67942
Matrix condition is 32.198
Found 149955 points in label.
Pruning voxels by thr: 0.000000
Found 148274 voxels in mask
Saving mask to lh.rmanova/mask.mgh
Reshaping mriglm->mask...
search space = 73670.427324
MatrixReadTxT: could not scan value [2][1]
ERROR: loading C tp1_vs_tp2.mtx
Any help would be greatly appreciated.
Thanks,
Harry