Why are you doing your own MC simulation? You can just use the tables
that we distribute ...
On 1/17/18 6:12 PM, miracle ozzoude wrote:
Hello Experts,
I am running a paired t-test cortical thickness analysis based on the
instruction on the wiki page
(https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis). However,
the monte carlo files weren't not created when i corrected for
multiple comparisons. Below are my script, fsgd files, mc-z log file,
and a screenshot of contrast folder missing mc.z maps. Please can you
help me figure out why the error is happening. Thank you.
Best,
Paul
*Script*:
pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx
martrix2=age.mtx
#resample each subjects's left and right hemisphere data to fsavarage.
mris_preproc --target fsaverage --hemi lh --meas thickness --out
lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
mris_preproc --target fsaverage --hemi rh --meas thickness --out
rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
# #smoothen the concatenated file by 5mm FWHM. --cortex means only
smooth areas in the cortex. N:B. FWHM changes based on study type.
mri_surf2surf --hemi lh --s fsaverage --sval
lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval
lh.paired-diff.thickness.sm05.mgh
mri_surf2surf --hemi rh --s fsaverage --sval
rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval
rh.paired-diff.thickness.sm05.mgh
# #Run GLM analysis
mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired --C
$martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir
lh.paired-diff.glmdirir
mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired --C
$martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir
rh.paired-diff.glmdir
# # #Run Clusterwise correction for multiple comparisons using MONTE
CARLO. First create a table for of simulations
mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 10000 2
mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 10000 2
mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
*Fsgd file 1:pairs.fsgd*
GroupDescriptorFile 1
Class ADEX
Input 1000_1 ADEX
Input 1000_2 ADEX
Input 1001_1 ADEX
Input 1001_2 ADEX
Input 1003_1 ADEX
Input 1003_2 ADEX
Input 1005_1 ADEX
Input 1005_2 ADEX
Input 1008_1 ADEX
Input 1008_2 ADEX
Input 1013_1 ADEX
Input 1013_2 ADEX
Input 1014_1 ADEX
Input 1014_2 ADEX
*Fsgd file 2: paired_diff.fsgd*
GroupDescriptorFile 1
Class ADEX
Variables Age
Input 1000 ADEX 72
Input 1001 ADEX 76
Input 1003 ADEX 72
Input 1005 ADEX 80
Input 1008 ADEX 72
Input 1013 ADEX 80
Input 1014 ADEX 80
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