I'm running a monte carlo sim and am getting an error:
command line:
mri_glmfit-sim \
--glmdir MTA_persistanceCP \
--sim mc-z 1000 1.3 mc-z.negative \
--sim-sign abs --cwpvalthresh 0.999 \
--overwrite
output:
cmdline mri_glmfit --y /Studies/MTA/qdec/MTA_persistanceCP/y.mgh --fsgd /Studies/MTA/qdec/MTA_persistanceCP/qdec.fsgd dods --glmdir /Studies/MTA/qdec/MTA_persistanceCP --surf fsaverage rh --label /Studies/MTA/fsaverage/label/rh.aparc.label --C /Studies/MTA/qdec/MTA_persistanceCP/contrasts/rh-Avg-Intercept-thickness.mat
--C /Studies/MTA/qdec/MTA_persistanceCP/contrasts/rh-Diff-F-M-Intercept-thickness.mat
SURFACE: fsaverage rh
log file is MTA_persistanceCP/mc-z.negative.mri_glmfit-sim.log
cd /Studies/MTA/qdec
/Applications/freesurfer/bin/mri_glmfit-sim
--glmdir MTA_persistanceCP --sim mc-z 1000 1.3 mc-z.negative --sim-sign abs --cwpvalthresh 0.999 --overwrite
$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
Tue Jul 29 14:08:52 CDT 2014
Darwin psy-blackbird.ad.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
wieser
setenv SUBJECTS_DIR /Applications/freesurfer/subjects
FREESURFER_HOME /Applications/freesurfer
Original mri_glmfit command line:
cmdline mri_glmfit --y /Studies/MTA/qdec/MTA_persistanceCP/y.mgh --fsgd /Studies/MTA/qdec/MTA_persistanceCP/qdec.fsgd dods --glmdir /Studies/MTA/qdec/MTA_persistanceCP --surf fsaverage rh --label /Studies/MTA/fsaverage/label/rh.aparc.label --C /Studies/MTA/qdec/MTA_persistanceCP/contrasts/rh-Avg-Intercept-thickness.mat
--C /Studies/MTA/qdec/MTA_persistanceCP/contrasts/rh-Diff-F-M-Intercept-thickness.mat
DoSim = 1
UseCache = 0
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 14.370530
nSimPerJob = 1000
1/1 Tue Jul 29 14:08:52 CDT 2014
mri_glmfit --y MTA_persistanceCP/y.mgh --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Avg-Intercept-thickness.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Avg-thickness-Gender-Cor.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-C-P-Cor-thickness-Gender.mtx
--C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-C-P-Intercept-thickness.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-Control-MJuser-Cor-thickness-Gender.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-Control-MJuser-Intercept-thickness.mtx
--C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-F-M-Intercept-thickness.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-X-ADHD_Persist-MJ_group-Cor-thickness-Gender.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-X-ADHD_Persist-MJ_group-Intercept-thickness.mtx
--C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Avg-Intercept-thickness.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Avg-thickness-Gender-Cor.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-C-P-Cor-thickness-Gender.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-C-P-Intercept-thickness.mtx
--C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-Control-MJuser-Cor-thickness-Gender.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-Control-MJuser-Intercept-thickness.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-F-M-Intercept-thickness.mtx
--C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-X-ADHD_Persist-MJ_group-Cor-thickness-Gender.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-X-ADHD_Persist-MJ_group-Intercept-thickness.mtx --mask MTA_persistanceCP/mask.mgh --sim mc-z 1000 1.3 MTA_persistanceCP/csd/mc-z.negative.j001
--sim-sign abs --fwhm 14.370530 --fsgd MTA_persistanceCP/y.fsgd dods --label /Studies/MTA/fsaverage/label/rh.aparc.label --surf fsaverage rh white
INFO: ignoring tag Creator
INFO: ignoring tag SUBJECTS_DIR
INFO: ignoring tag SynthSeed
simbase MTA_persistanceCP/csd/mc-z.negative.j001
FWHM = 14.370530
gdfReadHeader: reading MTA_persistanceCP/y.fsgd
INFO: NOT demeaning continuous variables
Continuous Variable Means (all subjects)
0 Age 23.9348 1.40499
Class Means of each Continuous Variable
1 Gender_MFF 23.8000
2 Gender_MFM 23.9722
INFO: gd2mtx_method is dods
Reading source surface /Applications/freesurfer/subjects/fsaverage/surf/rh.white
Number of vertices 163842
Number of faces 327680
Total area 65020.765625
AvgVtxArea 0.396850
AvgVtxDist 0.717994
StdVtxDist 0.193566
Surface smoothing by fwhm=14.370530, niters=152.000000
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /Studies/MTA/Qdec
cmdline mri_glmfit --y MTA_persistanceCP/y.mgh --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Avg-Intercept-thickness.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Avg-thickness-Gender-Cor.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-C-P-Cor-thickness-Gender.mtx
--C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-C-P-Intercept-thickness.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-Control-MJuser-Cor-thickness-Gender.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-Control-MJuser-Intercept-thickness.mtx
--C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-F-M-Intercept-thickness.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-X-ADHD_Persist-MJ_group-Cor-thickness-Gender.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-X-ADHD_Persist-MJ_group-Intercept-thickness.mtx
--C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Avg-Intercept-thickness.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Avg-thickness-Gender-Cor.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-C-P-Cor-thickness-Gender.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-C-P-Intercept-thickness.mtx
--C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-Control-MJuser-Cor-thickness-Gender.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-Control-MJuser-Intercept-thickness.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-F-M-Intercept-thickness.mtx
--C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-X-ADHD_Persist-MJ_group-Cor-thickness-Gender.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-X-ADHD_Persist-MJ_group-Intercept-thickness.mtx --mask MTA_persistanceCP/mask.mgh --sim mc-z 1000 1.3 MTA_persistanceCP/csd/mc-z.negative.j001
--sim-sign abs --fwhm 14.370530 --fsgd MTA_persistanceCP/y.fsgd dods --label /Studies/MTA/fsaverage/label/rh.aparc.label --surf fsaverage rh white
sysname Darwin
hostname psy-blackbird.ad.uwm.edu
machine x86_64
user wieser
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
fwhm 14.370530
niters 152.000000
OneSampleGroupMean 0
y /Studies/MTA/Qdec/MTA_persistanceCP/y.mgh
logyflag 0
usedti 0
FSGD MTA_persistanceCP/y.fsgd
labelmask /Studies/MTA/fsaverage/label/rh.aparc.label
maskinv 0
glmdir (null)
IllCondOK 0
ReScaleX 1
DoFFx 0
Loading y from /Studies/MTA/Qdec/MTA_persistanceCP/y.mgh
INFO: gd2mtx_method is dods
Normalized matrix condition is 1366.76
Matrix condition is 712602
Found 148495 points in label.
Found 148495 voxels in mask
Reshaping mriglm->mask...
search space = 73776.320066
ERROR: dimension mismatch between X and contrast MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Avg-thickness-Gender-Cor.mtx X has 4 cols, C has 12 cols
How do I fix this dimension masmatch?
thanks
Jon