you have an extra blank line in your contrast matrix On 04/19/2014 11:41 PM, Harry Hallock [hhal5...@uni.sydney.edu.au] wrote: > > 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 > > > *Harry Hallock*| MPhil Candidate > Regenerative Neuroscience Group | Brain & Mind Research Institute > *THE UNIVERSITY OF SYDNEY* > > Room 408, Level 4, M02K | 94 Mallett St Camperdown | NSW | 2050| Australia > *T +*61 2 9114 4138 F +61 9351 0930 > *E *hhal5...@uni.sydney.edu.au*| W *www.rng.org.au > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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