Thank you! I completely didn't see that. It worked. I was wondering how to proceed next. The tutorial ends with running the glmfit command. I've tried correcting for multiple comparisons with Monte Carlo but that doesn't seem to work. How can I interpret the files that are the output from the repeated measures ANOVA?
Cheers Clara ----- Ursprüngliche Mail ----- Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 29. März 2017 18:15:57 Betreff: Re: [Freesurfer] glmfit mismatch between X and C with same no of columns Since there are 40 subjects, you would only have 40+1 columns, not 80+1 On 03/29/2017 03:42 AM, Clara Kühn wrote: > Hi Doug, > > I've also attached the fsgd file for you. Yes, I have 40 subjects and a > contrast column. I adapted this from this tutorial: > https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova where the > example has 3 time points and therefore 2 contrast columns. Since I want to > look at only 2 I only have one contrast column which is also my 81st column > in the contrast matrix. > > Did I adapt it in a wrong way for my 2 timepoints? > Cheers > Clara > > ----- Ursprüngliche Mail ----- > Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> > An: freesurfer@nmr.mgh.harvard.edu > Gesendet: Dienstag, 28. März 2017 18:37:58 > Betreff: Re: [Freesurfer] glmfit mismatch between X and C with same no of > columns > > I'm not sure what's in your FSGD file, but you design matrix has 41 > columns and your contrast matrix has 80. I'm guessing that you have 40 > subjects and that you created the contrast matrix based on DODS and not > DOSS (see the web page on the rmanova about creating contrasts) > > > On 03/28/2017 03:50 AM, Clara Kühn wrote: >> Sorry, I had a typo in the fsgd file. This is the correct command line and >> terminal output: >> >> mri_glmfit --glmdir $SUBJECTS_DIR/qdec/rmanova/ --y >> $SUBJECTS_DIR/81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh >> --fsgd $SUBJECTS_DIR/qdec/rmanova/2014.03.27-40kids-rmanova.fsgd doss --C >> $SUBJECTS_DIR/qdec/rmanova/C-pre-vs-post.mtx >> >> >> gdfReadHeader: reading >> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/2014.03.27-40kids-rmanova.fsgd >> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. >> Continuous Variable Means (all subjects) >> 0 pre-vs-post 0 1 >> Class Means of each Continuous Variable >> 1 Subject1 0.0000 >> 2 Subject2 0.0000 >> 3 Subject3 0.0000 >> 4 Subject4 0.0000 >> 5 Subject5 0.0000 >> 6 Subject6 0.0000 >> 7 Subject7 0.0000 >> 8 Subject8 0.0000 >> 9 Subject9 0.0000 >> 10 Subject10 0.0000 >> 11 Subject11 0.0000 >> 12 Subject12 0.0000 >> 13 Subject13 0.0000 >> 14 Subject14 0.0000 >> 15 Subject15 0.0000 >> 16 Subject16 0.0000 >> 17 Subject17 0.0000 >> 18 Subject18 0.0000 >> 19 Subject19 0.0000 >> 20 Subject20 0.0000 >> 21 Subject21 0.0000 >> 22 Subject22 0.0000 >> 23 Subject23 0.0000 >> 24 Subject24 0.0000 >> 25 Subject25 0.0000 >> 26 Subject26 0.0000 >> 27 Subject27 0.0000 >> 28 Subject28 0.0000 >> 29 Subject29 0.0000 >> 30 Subject30 0.0000 >> 31 Subject31 0.0000 >> 32 Subject32 0.0000 >> 33 Subject33 0.0000 >> 34 Subject34 0.0000 >> 35 Subject35 0.0000 >> 36 Subject36 0.0000 >> 37 Subject37 0.0000 >> 38 Subject38 0.0000 >> 39 Subject39 0.0000 >> 40 Subject40 0.0000 >> INFO: gd2mtx_method is doss >> >> $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ >> cwd /home/raid2/ckuehn >> cmdline mri_glmfit --glmdir >> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/ --y >> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh >> --fsgd >> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/2014.03.27-40kids-rmanova.fsgd >> doss --C >> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post.mtx >> sysname Linux >> hostname parana >> machine x86_64 >> user ckuehn >> FixVertexAreaFlag = 1 >> UseMaskWithSmoothing 1 >> OneSampleGroupMean 0 >> y >> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh >> logyflag 0 >> usedti 0 >> FSGD >> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/2014.03.27-40kids-rmanova.fsgd >> glmdir /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/ >> IllCondOK 0 >> ReScaleX 1 >> DoFFx 0 >> Creating output directory >> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/ >> Loading y from >> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh >> INFO: gd2mtx_method is doss >> Saving design matrix to >> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova//Xg.dat >> Normalized matrix condition is 1 >> Matrix condition is 40 >> Pruning voxels by thr: 0.000000 >> Found 97361 voxels in mask >> Saving mask to >> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova//mask.mgh >> search space = 97361.000000 >> ERROR: dimension mismatch between X and contrast >> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post.mtx >> X has 41 cols, C has 81 cols >> >> >> ----- Ursprüngliche Mail ----- >> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> >> An: freesurfer@nmr.mgh.harvard.edu >> Gesendet: Montag, 27. März 2017 19:49:04 >> Betreff: Re: [Freesurfer] glmfit mismatch between X and C with same no of >> columns >> >> Need command line and terminal output >> >> >> On 03/27/2017 09:08 AM, Clara Kühn wrote: >>> Dear Freesurfer experts, >>> >>> I'm trying to run a repeated measures anova as described here: >>> https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova >>> >>> I have 40 subjects with 2 time points each, so it's quite a large matrix. >>> When running the mri_glmfit command I get the following error: >>> >>> ERROR: dimension mismatch between X and contrast >>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post.mtx >>> X has 41 cols, C has 81 cols >>> >>> I'm not sure what to do as the matrix and the contrast (see attachments) >>> actually have the same amount of columns... >>> >>> Any help would be much appreciated, thank you! >>> Clara >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. 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