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