Hi Doug,
Below is the output in the terminal window from running the analysis to the crash. Attached are the qdec.fsgd and y.fsgd files from the qdec output. I'm not actually sure what these file represent - could you enlighten me?
Thanks! Laura.
Number of subjects: 55 Number of factors: 48 (2 discrete, 46 continuous) Number of classes: 4 Number of regressors: 188 ============================================================
WARNING: will exclude subject 27115 from analysis due to NaN data point!
WARNING: will exclude subject 27211 from analysis due to NaN data point!
WARNING: will exclude subject 27212 from analysis due to NaN data point! lh-Avg-Intercept-thickness ----------------------- Does the average thickness differ from zero? Nuisance factors: IntraCranialVol 1.000 1.000 0.000 0.000 0.000 0.000;
lh-Avg-thickness-CPT_IP-Cor ----------------------- Does the correlation between thickness and CPT_IP, accounting for group, differ from zero? Nuisance factors: IntraCranialVol 0.000 0.000 1.000 1.000 0.000 0.000;
lh-Diff-HC-SZ-Intercept-thickness ----------------------- Does the average thickness differ between HC and SZ? Nuisance factors: IntraCranialVol 1.000 -1.000 0.000 0.000 0.000 0.000;
lh-Diff-HC-SZ-Cor-thickness-CPT_IP ----------------------- Does the thickness--CPT_IP correlation differ between HC and SZ? Nuisance factors: IntraCranialVol 0.000 0.000 1.000 -1.000 0.000 0.000;
ninputs = 52 Checking inputs nframestot = 52 Allocing output Done allocing nframes = 52 Writing to /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/y.mgh gdfReadHeader: reading /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/qdec.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 CPT_IP 2.83135 0.695203 1 IntraCranialVol 1.29955e+06 249396 Class Means of each Continuous Variable 1 groupHC 3.0515 1340186.4398 2 groupSZ 2.5936 1255661.8075 INFO: gd2mtx_method is dods Reading source surface /ncf/snp/04/SCORE/freesurfer_analysis/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 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /ncf/snp/04/SCORE/freesurfer_analysis/qdec cmdline mri_glmfit --y /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/y.mgh --fsgd /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/qdec.fsgd dods --glmdir /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV --surf fsaverage lh --label /ncf/snp/04/SCORE/freesurfer_analysis/fsaverage/label/lh.aparc.label --C /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/contrasts/lh-Avg-Intercept-thickness.mat --C /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/contrasts/lh-Avg-thickness-CPT_IP-Cor.mat --C /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/contrasts/lh-Diff-HC-SZ-Intercept-thickness.mat --C /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/contrasts/lh-Diff-HC-SZ-Cor-thickness-CPT_IP.mat
sysname Linux hostname ncfws17.rc.fas.harvard.edu machine x86_64 user ltully FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/y.mgh logyflag 0 usedti 0 FSGD /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/qdec.fsgd labelmask /ncf/snp/04/SCORE/freesurfer_analysis/fsaverage/label/lh.aparc.label maskinv 0 glmdir /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV Loading y from /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/y.mgh INFO: gd2mtx_method is dods Saving design matrix to /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/Xg.dat Normalized matrix condition is 263.453 Matrix condition is 1e+08 Found 148151 points in label. Pruning voxels by thr: 0.000000 Found 148025 voxels in mask Saving mask to /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/mask.mgh Reshaping mriglm->mask... search space = 73649.347769 DOF = 46 Starting fit and test Fit completed in 0.11535 minutes Computing spatial AR1 on surface Residual: ar1mn=0.996105, ar1std=0.001362, gstd=6.478212, fwhm=15.255024 Writing results lh-Avg-Intercept-thickness maxvox sig=21.5032 F=315.736 at index 99361 0 0 seed=1330929601 lh-Avg-thickness-CPT_IP-Cor maxvox sig=3.23567 F=13.661 at index 155907 0 0 seed=1330929601 lh-Diff-HC-SZ-Intercept-thickness maxvox sig=-2.63051 F=10.3802 at index 6941 0 0 seed=1330929601 lh-Diff-HC-SZ-Cor-thickness-CPT_IP maxvox sig=-3.05362 F=12.6489 at index 145301 0 0 seed=1330929601 mri_glmfit done ninputs = 4 Checking inputs nframestot = 4 Allocing output Done allocing nframes = 4 Writing to /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/contrasts.sig.mgh reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) gdfReadHeader: reading /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10mm_groupCPT_ICV/y.fsgd INFO: ignoring tag Creator INFO: ignoring tag SUBJECTS_DIR INFO: ignoring tag SynthSeed INFO: NOT demeaning continuous variables Continuous Variable Means (all subjects) 0 CPT_IP 2.83135 0.695203 1 IntraCranialVol 1.29955e+06 249396 Class Means of each Continuous Variable 1 groupHC 3.0515 1340187.1111 2 groupSZ 2.5936 1255662.3200 MatrixMultiply: m1 is null!
No such file or directory
On Tue, Feb 28, 2012 at 5:51 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Can you send the fsgd file that is created? Also, please send more text output. It's hard to tell from a single line. doug
Laura Tully wrote:
Hi, I am trying to run a between group analysis in QDEC whilst controlling for intrancranial volume. The design has one dichotomous variable (group2, group2), one continuous (performance on behavioral task), and one nuisance variable (intracranial volume). each time I run it qec crashes with the following error: MatrixMultiply: ml null!
What does this error mean and how can I fix it? What is odd is that this error does not seem to be consistently reproducible - after successfully running the analyses without controlling for ICV, I was then able to run it with ICV as a nuisance factor. Thank you! Laura. -- Laura Tully Social Neuroscience & Psychopathology Harvard University 806 William James Hall 33 Kirkland St Cambridge, MA 02138 ltully@fas.harvard.edu mailto:ltully@fas.harvard.edu**
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