Hi Doug, do you think it will be possible for you to fix that bug in a week or so? It's somewhat crucial for my analysis.
Another thing I'd like to ask is: how feasible would it be to implement the --min operation into mri_concat? There is already a --max to compute the max of concatenated volumes, but I have to use fscalc.fsl to get the minimum of the inputs to calculate conjunctions (like Thomas Nichols recommended). So far so good. The problem I noticed is, since the surface has to be transformed into a volume and back, maybe due to some truncation effects the output surface is slightly different from the input (I dont mean the operation itself) and won't match to a mask anymore. In other words: the signal looks the same, but masking will fail. There are two options to get around this: doing the masking with fscalc.fsl or apply a dummy operation to the mask with fscalc.fsl to "shift" the mask the same way as the signal and then do the masking with mri_mask. Therefore I ask because the calculations with mri_concat would be much faster and it seems slightly more accurate, too. What do you think? Thanks again and sorry for the constant spamming... Georg -----Ursprüngliche Nachricht----- Von: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Gesendet: Montag, 20. Juli 2009 21:10 An: Georg Homola Cc: 'Freesurfer Mailing List' Betreff: Re: [Freesurfer] Three classes and GLM / mri_glmfit dof bug It probably won't change it that much as it's just a t or F test. doug Georg Homola wrote: > Hi Doug, > > so it should also be easily possible to compare only two runs of one subject > as I initially wanted to do it. To compute the weighted combination would be > a hell of a work for me, since I got almost 30 subjects with lots of copes > and even more contrasts, so I would have to do that for more than a thousand > variations manually (although partly scriptable). > > I'd rather wait for the bugfix, if that's not going to take too long. Or is > there an older version of mri_glmfit without that bug I could use only for > the fixed effects part of my analysis? > > A subsequent question for me is, how important is the exact number of dofs > for mri_glmfit (or for the GLM in general) anyway? Since I got varying sums > of dofs esp. because of motion outliers, I cumulated the dofs for every > single case. The sums are in a range from 835 to 908. Now, could I just pass > mri_glmfit (without that bug) the lowest number to stick with it, even > though there are a bit more dofs in some cases, or would that change any > results? > > Thank you very much for your help in advance! > Best regards, > Georg > > > > -----Ursprüngliche Nachricht----- > Von: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N > Greve > Gesendet: Freitag, 17. Juli 2009 20:04 > An: Georg Homola > Cc: 'Freesurfer Mailing List' > Betreff: Re: [Freesurfer] Three classes and GLM > > This is a bug in mri_glmfit in that it does not recognize that the dof > is really 884 and not 0. The easiest thing to do right now is to > explicitly compute the weighted combination, then do an osgm. You can > use fscalc.fsl to do this. > > doug > > > > Georg Homola wrote: > >> Hi all, >> >> I'm having some problems getting a second level fixed effects analysis >> started on my subjects. There are three runs (dofsum = 884) in each case >> > I'd > >> like to compare. >> >> OSGM works fine so far, but when I apply a matrix like this: >> >> 1 0 0 >> 0 1 0 >> 0 0 1 >> >> To a contrast like that: >> >> 0.5 0.5 -1 >> >> mri_glmfit tells me: ERROR DOF = 0. >> >> I also tried it with an FSGD file, so my approach was the same as for the >> Fsgdf3G0V example (http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V). >> > That > >> makes no difference. >> >> When I divide the three runs into two classes, everything works fine >> > again. > >> But why the error with three classes? >> >> Any ideas? >> >> Thanks, >> Georg >> >> >> >> $ mri_glmfit --surf 01 lh --y 01/gender.lh.cope1.sm05.mgz --yffxvar >> 01/gender.lh.varcope1.sm05.mgz --ffxdof 884 --glmdir >> 01/results/gender.sm05.lh --X xmat.mat --C test.mat --label >> $SUBJECTS_DIR/01/label/lh.cortex.label >> Reading source surface /data/freesurfer/01/surf/lh.white >> Number of vertices 149696 >> Number of faces 299388 >> Total area 96879.085938 >> AvgVtxArea 0.647172 >> AvgVtxDist 0.880017 >> StdVtxDist 0.256396 >> >> $Id: mri_glmfit.c,v 1.138.2.10 2009/05/18 15:41:44 greve Exp $ >> cwd /data/freesurfer/higher/highest/fixed >> cmdline mri_glmfit --surf 01 lh --y 01/gender.lh.cope1.sm05.mgz --yffxvar >> 01/gender.lh.varcope1.sm05.mgz --ffxdof 884 --glmdir >> 01/results/gender.sm05.lh --X xmat.mat --C test.mat --label >> /data/freesurfer/01/label/lh.cortex.label >> sysname Darwin >> FixVertexAreaFlag = 1 >> UseMaskWithSmoothing 1 >> OneSampleGroupMean 0 >> y /data/freesurfer/higher/highest/fixed/01/gender.lh.cope1.sm05.mgz >> logyflag 0 >> X xmat.mat >> usedti 0 >> labelmask /data/freesurfer/01/label/lh.cortex.label >> maskinv 0 >> glmdir 01/results/gender.sm05.lh >> IllCondOK 0 >> DoFFx 1 >> FFxDOF 884 >> yFFxVar >> > /data/freesurfer/higher/highest/fixed/01/gender.lh.varcope1.sm05.mgz > >> Creating output directory 01/results/gender.sm05.lh >> Loading y from >> /data/freesurfer/higher/highest/fixed/01/gender.lh.cope1.sm05.mgz >> Loading yffxvar from >> /data/freesurfer/higher/highest/fixed/01/gender.lh.varcope1.sm05.mgz >> Saving design matrix to 01/results/gender.sm05.lh/Xg.dat >> Matrix condition is 1 >> /data/freesurfer/01/label/lh.cortex.label >> /data/freesurfer/01/label/lh.cortex.label >> Found 141245 points in label. >> Pruning voxels by thr: 0.000000 >> Found 141245 voxels in mask >> Saving mask to 01/results/gender.sm05.lh/mask.mgh >> search space = 91409.8 >> DOF = 0 >> ERROR: DOF = 0 >> >> >> >> _______________________________________________ >> 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
