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 <gr...@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/ > > 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 <gr...@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 <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.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 >>> >>> >>> _______________________________________________ >>> 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. >>> >>> >> >> >> _______________________________________________ >> 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. >> >> > > > _______________________________________________ > 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. > >
_______________________________________________ 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.
