Hi Doug I am not conciously using a mask but I attached the glmfit.log At the end it actually states "ResidualFWHM -nan"
How can I fix that? Cheers, Clara ----- Ursprüngliche Mail ----- Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> An: freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 10. April 2017 21:41:40 Betreff: Re: [Freesurfer] glmfit mismatch between X and C with same no of columns It estimates the FWHM from the residuals of the analysis (it does not use whatever value you smoothed it with). For some reason this estimate is not-a-number (NaN). Are you using a mask? Can you send the terminal output from running mri_glmfit? On 03/31/2017 03:29 AM, Clara Kühn wrote: > ah, ok. I used the proper glmdir now with this command: > mri_glmfit-sim --glmdir > /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/qdec/rmanova/ > --cache-dir > /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//average/mult-comp-cor/ > --cache 3.0 abs --cwp 0.05 --2spaces > > And this is the terminal output: > > 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/2017.03.27-40kids-rmanova.fsgd > doss --C > /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post.mtx > > WARNING: unrecognized mri_glmfit cmd option doss > > log file is > /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/qdec/rmanova//cache.mri_glmfit-sim.log > > cd /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2 > /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64/bin/mri_glmfit-sim > --glmdir /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/qdec/rmanova/ > --cache-dir > /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//average/mult-comp-cor/ > --cache 3.0 abs --cwp 0.05 --2spaces > > $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ > Fri Mar 31 09:17:53 CEST 2017 > Linux etsch 4.4.0-66-generic #87-Ubuntu SMP Fri Mar 3 15:29:05 UTC 2017 > x86_64 x86_64 x86_64 GNU/Linux > ckuehn > setenv SUBJECTS_DIR /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/ > FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64 > > Original mri_glmfit command line: > 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/2017.03.27-40kids-rmanova.fsgd > doss --C > /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post.mtx > > DoSim = 0 > UseCache = 1 > DoPoll = 0 > DoPBSubmit = 0 > DoBackground = 0 > DiagCluster = 0 > gd2mtx = doss > fwhm = -nan > ERROR: cannot find > /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//average/mult-comp-cor////cortex/fwhmNaN/abs/th30/mc-z.csd > > > > For some reason it doesn't recognize that I smoothed the data with --fwhm 10 > during mris_surf2surf. And the other thing is, that it doesn't find the > correct path for the mc-z.csd. It should be in > /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//average/mult-comp-cor/81kids_template/lh/cortex/fwhm10/abs/mc-z.csd > > Cheers > Clara > > ----- Ursprüngliche Mail ----- > Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> > An: freesurfer@nmr.mgh.harvard.edu > Gesendet: Donnerstag, 30. März 2017 19:13:43 > Betreff: Re: [Freesurfer] glmfit mismatch between X and C with same no of > columns > > you are not giving it the proper glmdir dir. the glmdir is > > /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova > > > On 03/30/2017 01:12 PM, Clara Kühn wrote: >> 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.
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2 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/2017.03.27-40kids-rmanova.fsgd doss --C /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post.mtx sysname Linux hostname etsch 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/2017.03.27-40kids-rmanova.fsgd glmdir /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/ IllCondOK 0 ReScaleX 1 DoFFx 0 ResidualFWHM -nan SearchSpace 97361.000000 anattype volume
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