I've seen this happen if two analyses were run using the same output directory. Some of the contrasts won't get deleted the 2nd time it is run.
doug
Nick Schmansky wrote:
Rosa,
Was this script generated after an analysis was successfully run? You will need to run an analysis first (ie, selecting your factors, etc, press Analyze, then select a contrast for display in the Display tab), then you can use the mri_glmfit-sim script generator feature.
I can't think of a reason why the design matrix and contrast matrix columns are different.
Nick
On Thu, 2009-07-30 at 11:17 +0200, Rosa Steimke wrote:
HI Nick!
I generated and ran the scribt, but it gives me following error message:
ERROR: dimension mismatch between X and contrast /Users/steimke/Rosa_MRTs/qdec/Untitled/tmp.mri_glmfit-sim-77641/lh-Avg-thickness-Age-Cor.mtx X has 2 cols, C has 12 cols
I have to admitt that I did not really understand wether I had to change anything in the scribt or whether i ould leave it like it is? thanks for your help! Rosa
-------- Original-Nachricht --------
Datum: Fri, 24 Jul 2009 17:16:27 -0400 Von: Nick Schmansky nicks@nmr.mgh.harvard.edu An: Rosa Steimke rosasteimke@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] clusterwise correction for multiple comparison
Rosa,
If you have the newest version of qdec, it has a button to generate the mri_glmfit-sim script for you, with the proper directory input and output generated for you.
You'll still have to load the results on your own in tksurfer by following these instructions:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#Clusterwis...
Nick
On Fri, 2009-07-24 at 13:48 +0200, Rosa Steimke wrote:
HI! i have a question regarding multiple comparion correction in qdec. can i
use a clusterwise correction?
i found the following script for glm:
mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --sim mc-z 5 4 mc-z.negative \ --sim-sign neg \ --overwrite
but i dont understand how i should apply it in qdec. what shoudl i use
as input directory?
rosa
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