Hi all, I am conducting a contrast of z (r) maps from 3 seed-based resting-state networks (e.g., 1 > 2 and 3). To eliminate the influence of anticorrelations on the contrast results, I thresholded the z (r) maps at 0 before running mri_glmfit, thereby eliminating voxels with negative z (r) values. The command completed successfully but the resulting sig maps did not contain voxels with any values. I have attached the fsgd and contrast files and pasted the command and output below. Can anyone identify the problem here? Thanks, Kevin
*Potentially problematic portion of output:*
Pruning voxels by thr: 0.000000
Found 0 voxels in mask
Saving mask to LR_Amy_lOFC2_glm2/mask.mgh
search space = 0.000000
*Entire command and output: *
[kreature:kbickart_fcmap_ASN_Anchor_AmyPks_buckner_YC] (nmr-stable5.1-env)
mri_glmfit --y LR_Amy_lOFCpk2
_vs_vmPFCpk2_and_cACCpk2_pos_4D.nii.gz --allowsubjrep --fsgd
/autofs/homes/006/kbickart/AmySubNet_glm/pa
ired3.fsgd doss --C /autofs/homes/006/kbickart/AmySubNet_glm/paired.mat
--glmdir LR_Amy_lOFC2_glm2
gdfReadHeader: reading /autofs/homes/006/kbickart/AmySubNet_glm/paired3.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 roi1_vs_roi2_vs_roi3 0 0.707107
Class Means of each Continuous Variable
1 Class_081028_BC77WB 0.0000
2 Class_081028_XE45TK 0.0000
3 Class_081028_YY28TK 0.0000
....
$Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $
cwd
/autofs/cluster/animal/rs-fmri/YC/GROUP_STATS/kbickart/FCMAP/kbickart_fcmap_ASN_Anchor_AmyPks_buckne
r_YC
cmdline mri_glmfit --y LR_Amy_lOFCpk2_vs_vmPFCpk2_and_cACCpk2_pos_4D.nii.gz
--allowsubjrep --fsgd /autof
s/homes/006/kbickart/AmySubNet_glm/paired3.fsgd doss --C
/autofs/homes/006/kbickart/AmySubNet_glm/paired
.mat --glmdir LR_Amy_lOFC2_glm2
sysname Linux
hostname kreature
machine x86_64
user kbickart
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y
/autofs/cluster/animal/rs-fmri/YC/GROUP_STATS/kbickart/FCMAP/kbickart_fcmap_ASN_Anchor_AmyPks_buckn
er_YC/LR_Amy_lOFCpk2_vs_vmPFCpk2_and_cACCpk2_pos_4D.nii.gz
logyflag 0
usedti 0
FSGD /autofs/homes/006/kbickart/AmySubNet_glm/paired3.fsgd
glmdir LR_Amy_lOFC2_glm2
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory LR_Amy_lOFC2_glm2
Loading y from
/autofs/cluster/animal/rs-fmri/YC/GROUP_STATS/kbickart/FCMAP/kbickart_fcmap_ASN_Anchor_Am
yPks_buckner_YC/LR_Amy_lOFCpk2_vs_vmPFCpk2_and_cACCpk2_pos_4D.nii.gz
llINFO: gd2mtx_method is doss
Saving design matrix to LR_Amy_lOFC2_glm2/Xg.dat
Normalized matrix condition is 1
Matrix condition is 44.5
Pruning voxels by thr: 0.000000
Found 0 voxels in mask
Saving mask to LR_Amy_lOFC2_glm2/mask.mgh
search space = 0.000000
DOF = 177
Starting fit and test
Fit completed in 0.0148667 minutes
Computing spatial AR1 in volume.
fMRIspatialAR1(): hit 0 voxels
WARNING: no voxels in AR1 computation
Residual: ar1mn = (nan,nan,nan) fwhm = (nan,nan,nan) nan
Writing results
paired
maxvox sig=0 F=0 at index 0 0 0 seed=1321328111
mri_glmfit done
--
Kevin Bickart
MD-PhD Student
Department of Anatomy and Neurobiology
Boston University School of Medicine
live UP to it
paired3.fsgd
Description: Binary data
paired.mat
Description: Binary data
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