[Freesurfer] osgm and correction for multiple comparisons

2012-05-03 Thread Nicki Langer 

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
SynthSeed1315181525


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.lan...@psychologie.uzh.ch (email)
nicolas.langer[at]uzh.ch (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)




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[Freesurfer] mri_glmfit-sim on longitudinal data

2010-11-05 Thread Nicki Langer 

Hi,

I have read the Freesurfer Tutorial, but there is still something I do 
not understand.


I want to run the mri_glmfit-sim command on our data. I have one sample 
(10 subjects), which were examined at 2 different timepoints.


I tried to use this command:

mri_glmfit-sim --glmdir Plast_injury_Thickness_LH_sensorimotor.glmdir 
--sim mc-z 1000 2 lh_mz-z.abs --sim-sign abs --overwrite


The following error message occured:

y has 10 inputs, X has 20 Rows.

Although the X-file has only 10 rows (here is the content of the X file 
an y file)


X.mat =

1
1
1
1
1
1
1
1
1
1

y.fsgd =

GroupDescriptorFile 1
Title  InjuryInducedChanges

MeasurementName external
Tessellation surface
PlotFile 
/Applications/freesurfer/subjects/average/stats/glm/Plast_injury_lh_thickness.15.mgh

DesignMatFile X.mat dods
DeMeanFlag -1
ResidualFWHM 18.070986
LogY 0
Class injury
Input PlastInjur01_tp1.long.PlastInjur01 injury
Input PlastInjur01_tp2.long.PlastInjur01 injury
Input PlastInjur02_tp1.long.PlastInjur02 injury
Input PlastInjur02_tp2.long.PlastInjur02 injury
Input PlastInjur03_tp1.long.PlastInjur03 injury
Input PlastInjur03_tp2.long.PlastInjur03 injury
Input PlastInjur04_tp1.long.PlastInjur04 injury
Input PlastInjur04_tp2.long.PlastInjur04 injury
Input PlastInjur05_tp1.long.PlastInjur05 injury
Input PlastInjur05_tp2.long.PlastInjur05 injury
Input PlastInjur06_tp1.long.PlastInjur06 injury
Input PlastInjur06_tp2.long.PlastInjur06 injury
Input PlastInjur07_tp1.long.PlastInjur07 injury
Input PlastInjur07_tp2.long.PlastInjur07 injury
Input PlastInjur08_tp1.long.PlastInjur08 injury
Input PlastInjur08_tp2.long.PlastInjur08 injury
Input PlastInjur09_tp1.long.PlastInjur09 injury
Input PlastInjur09_tp2.long.PlastInjur09 injury
Input PlastInjur010_tp1.long.PlastInjur010 injury
Input PlastInjur010_tp2.long.PlastInjur010 injury

Creator  mri_glmfit
SUBJECTS_DIR /Applications/freesurfer/subjects
SynthSeed1289388591


What is exactly wrong? Or how do I apply the mri_glmfit-sim for 
longitudinal data correctly.


Thanks a lot for your help.

Best regards,

Nicolas
--

Nicolas Langer

MSc.UZH (lic. phil.)

Division Neuropsychology

Institute of Psychology

University of Zurich

Binzmuehlestrasse 14,

8050 Zurich, Switzerland

0041 44 635 73 92 (phone office)

0041 76 422 46 45 (phone mobile)

0041 44 635 74 09 (fax office)

BIN 4.D.04 (office room number)

nicolas.langer[at]uzh.ch (email)

http://www.psychologie.uzh.ch/neuropsy/ (website)

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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.