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
mc-z.abs.2.mri_glmfit-sim.log
Description: Binary data
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
