Hello Doug, I tried using the MC tables that FS distributed. However, i got an error about " cannot find /fwhm00/pos/th30/mc-z.csd ". I checked and there's no fwhm00, the table starts from fwhm01 to fwhm30. Below are my script and cache.mri_glmfi-sim.log files. My FreeSurfer version is stable version 5.3 on mac. Thank you.
Best, Paul mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex --cache 3 pos --cwpvalthresh 0.05 --2spaces --overwrite mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex --cache 3 pos --cwpvalthresh 0.05 --2spaces --overwrite On Thu, Jan 18, 2018 at 5:23 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > 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 > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > 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. > >
cache.mri_glmfit-sim.log
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