you have an extra blank line in your contrast matrix On 04/19/2014 11:41 PM, Harry Hallock [hhal5293@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 *hhal5293@uni.sydney.edu.au*| W *www.rng.org.au
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