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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
