On 08/05/2016 02:35 PM, miracoo...@gmail.com wrote: > Hello doug, > Should I add --label-src in addition to --label-trg or should I replace the > latter with the former? It does not matter as both the source and target are fsaveage > Thanks. Also, Just to conform, I should run mri_glmfit-sim after mri_mcsim. correct > Best, > Paul > > Sent from my BlackBerry 10 smartphone. > Original Message > From: Douglas N Greve > Sent: Friday, August 5, 2016 11:49 AM > To: freesurfer@nmr.mgh.harvard.edu > Reply To: Freesurfer support list > Subject: Re: [Freesurfer] group analysis/ region of interest (ROI) approach > > There are several things that need to be changed as I've indicated below > > On 08/01/2016 10:09 PM, miracle ozzoude wrote: >> Thanks doug. Also, Please can you verify if this are the right codes >> for performing ROI surface based analysis using the command line. I >> tried to reverse the whole brain analysis tutorial with some of the >> previous threads i read. I'm trying to mask the entorhinal and MT and >> then perform ROI on them using GLM. Thanks a lot >> >> CREATE MASK USING MRI_BINARIZE >> setenv SUJECTS_DIR users/paul/desktop/ims/fsaverage/mri >> cd users/paul/desktop/ims/fsaverage/mri >> mri_binarize --match [subjects] -i aparc+aseg.mgz -o lh.2mask.mgz >> >> MERGE TO LABELS >> cd users/paul/desktop/ims/fsaverage/label >> mri_mergelabels -i lh.entorhinal.label -i lh.MT.label -o lh.2mask.label >> >> MRIS_PREPROC >> cd users/paul/desktop/ims >> mris_preproc -fsgd filename.fsgd --target fsaverage hemi lh --meas >> thickness --out lh.filename.thickness.00.mgh >> >> MRI_SURF2SURF >> mri_surf2surf --hemi lh --s fsaverage --sval >> lh.filename.thickness.00.mgh --fwhm 10 --label-trg >> fsaverage/label/lh.2mask.label --tval lh.filename.thickness.10B.mgh > Add --label-src lh.2mask.label > This will cause it to smooth only in the mask >> GLM >> mri_glmfit --y lh.filename.thickness.10B.mgh --fsgd filname.fsgd dods >> --C contrastmatrix.mtx --surf fsaverage lh --label >> fsaverage/label/lh.2mask.label --glmdir lh.filename.glmdir >> >> CORRECTING FOR MULTIPLE COMPARISONS WITH MONTE CARLO 5000 iterations >> mri_glmfit-sim --glmdir lh.firstscore.glmdir --sim mc-z 5 2 >> mc-z.positive --sim-sign pos --cwpvalthresh 0.05 --2spaces > You will need to create your own correction simulation since you have > changed the search space. See here > http://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo >> On Mon, Aug 1, 2016 at 9:50 PM, Douglas Greve >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> I think there is an example on the wiki in the ROI analysis >> section. See >> >> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI >> >> After you run aparcstats2table, you can run mri_glmfit with >> --table aparcstatstable instead of --y. The output folder will >> have tables with lists of ROIs and p-values >> >> >> >> On 7/30/16 5:33 PM, miracle ozzoude wrote: >>> Hey FreeSurfer experts, >>> Does anyone know the steps i have to perform if I want to conduct >>> surface based thickness analysis using GLM but with ROI approach. >>> Thank you very much. >>> Best, >>> Paul >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> 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 >> >> >> 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
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