5 Feb
2018
5 Feb
'18
12:20 p.m.
The first frame in your input file is all 0s, so something is wrong with the fist subject
On 2/3/18 3:03 PM, miracle ozzoude wrote:
Hello Doug,
I have uploaded the files you requested. Thank you for your help.
Best, Paul
On Sat, Feb 3, 2018 at 1:53 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Can you upload the glmfit folders and the glmfit input (--y file) to our filedrop? https://gate.nmr.mgh.harvard.edu/filedrop2/ <https://gate.nmr.mgh.harvard.edu/filedrop2/> On 2/1/18 7:46 PM, miracle ozzoude wrote:Hello Doug, I have attached a screen shot of the mask.mgh for both right and left hemispheres. Everything looks yellow. I followed the paired t-test tutorial on the wiki page (included my scripts, fsgd files, and matrix in email thread). How do i go about fixing it? Thanks you Best, Paul On Tue, Jan 30, 2018 at 9:57 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: that usually means that something has gone wrong with the analysis. Do the maps look ok? In particular, look at the mask On 1/20/18 1:56 PM, miracle ozzoude wrote: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 <mailto: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.harvard.edu/fswiki/PairedAnalysis <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 list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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. 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