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" greve@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" greve@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" greve@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