Hi Nicolas, you should not have used both osgm and --fsgd in your original command line. If you had just used --fsgd, it would have failed with the same error msg. If you just use --osgm, both will succeed. doug
On 5/3/12 10:03 AM, Nicki Langer wrote:
Dear Freesurfer experts,
I've calculated a
I used the mri_glmfit for a one-sample group means (osgm) analysis:
mri_glmfit --y Tatool_lh_thickness.15.mgh --fsgd FSGD.txt --glmdir Tatool_Thickness_LH.glmdir --surf average lh --osgm --cortex
with following FSGD file:
GroupDescriptorFile 1 Title Tatool working_memory_group_young
MeasurementName external Tessellation surface PlotFile /Applications/freesurfer/subjects/average_tatool/stats/glm_wm_young/Tatool_lh_thickness.15.mgh DesignMatFile X.mat dods DeMeanFlag -1 ReScaleFlag 0 ResidualFWHM 21.999092 LogY 0 Class working_memory_group_young Input 20969474.long.20969474_base working_memory_group_young Input 20969474_T2.long.20969474_base working_memory_group_young Input 23912784.long.23912784_base working_memory_group_young Input 23912784_T2.long.23912784_base working_memory_group_young Input 25579161.long.25579161_base working_memory_group_young Input 25579161_T2.long.25579161_base working_memory_group_young Input 25793236.long.25793236_base working_memory_group_young Input 25793236_T2.long.25793236_base working_memory_group_young Input 27363346.long.27363346_base working_memory_group_young Input 27363346_T2.long.27363346_base working_memory_group_young Input 29378587.long.29378587_base working_memory_group_young Input 29378587_T2.long.29378587_base working_memory_group_young Input 29572758.long.29572758_base working_memory_group_young Input 29572758_T2.long.29572758_base working_memory_group_young Input 41282970.long.41282970_base working_memory_group_young Input 41282970_T2.long.41282970_base working_memory_group_young Input 45220481.long.45220481_base working_memory_group_young Input 45220481_T2.long.45220481_base working_memory_group_young Input 49925500.long.49925500_base working_memory_group_young Input 49925500_T2.long.49925500_base working_memory_group_young Input 52695504.long.52695504_base working_memory_group_young Input 52695504_T2.long.52695504_base working_memory_group_young Input 56064196.long.56064196_base working_memory_group_young Input 56064196_T2.long.56064196_base working_memory_group_young Input 56403386.long.56403386_base working_memory_group_young Input 56403386_T2.long.56403386_base working_memory_group_young Input 60241875.long.60241875_base working_memory_group_young Input 60241875_T2.long.60241875_base working_memory_group_young Input 75765433.long.75765433_base working_memory_group_young Input 75765433_T2.long.75765433_base working_memory_group_young Input 76596439.long.76596439_base working_memory_group_young Input 76596439_T2.long.76596439_base working_memory_group_young Creator mri_glmfit SUBJECTS_DIR /Applications/freesurfer/subjects SynthSeed 1315181525
In a second step, I tried to correct for mulitple comparisons by using the glmfit_sim:
mri_glmfit-sim --glmdir Tatool_Thickness_LH.glmdir --sim mc-z 5000 1.3 lh_mc-z.abs --sim-sign abs --overwrite
But there was the following errormessage:
ERROR: dimension mismatch between y and X. y has 16 inputs, X has 32 rows.
Has anybody solved this problem before?
(When I delete 16 rows of the FSGD file the simulation works, but then I don't trust the output anymore)
Thanks for your help.
Best,
Nicolas
Nicolas Langer MSc.UZH (lic. phil.) Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, 8050 Zurich, Switzerland 0041 44 635 73 96 (phone office) 0041 76 422 46 45 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) n.langer@psychologie.uzh.ch mailto:n.langer@psychologie.uzh.ch (email) nicolas.langer[at]uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website)
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