---------- Forwarded message ---------- From: miracle ozzoude miracooloz@gmail.com Date: Sat, Jan 20, 2018 at 1:56 PM Subject: Re: [Freesurfer] monte-carlo error in longitudinal pipeline To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
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 greve@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.harvar d.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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