I tried this command: mri_glmfit-sim --glmdir /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post --cache-dir /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//average/mult-comp-cor/ --cache 3.0 abs --cwp 0.05 --2spaces
and got this error: ERROR: cannot find /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post/mri_glmfit.log then I copied the .log file into the contrast directory C-pre-vs-post and tried the same command again and got this error: ERROR: could not determine file for /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post/mask Ususally I would run the MC on the lh-Diff-1-3-Intercept-long.area-spc folder but with the rmanova I get these two folders: 40kids-lh.thickness10-rmanova and C-pre-vs-post Cheers Clara ----- Ursprüngliche Mail ----- Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> An: freesurfer@nmr.mgh.harvard.edu Gesendet: Donnerstag, 30. März 2017 18:57:36 Betreff: Re: [Freesurfer] glmfit mismatch between X and C with same no of columns what do you mean that it did not seem to work? On 03/30/2017 11:25 AM, Clara Kühn wrote: > 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. 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
