If you are using version 6, you'll have to download the patch. But it is in version 7 already

On 6/8/2020 2:58 PM, Avi Gharehgazlou wrote:

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Hi experts,

I am trying to run permutation test on my lGI data using the command line below but I get an error saying “ERROR: Flag --perm-resid unrecognized”. I've ran my mri_glmfit command line with flag --eres-save (see below) and have installed and made executable the new version of mri_glmfit-sim as instructed here: (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0...) Will you please tell me how I can fix this?

permutation command line I used: mri_glmfit-sim --glmdir lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir --perm 1000 4.0 abs --perm-resid --cwp  0.05 --2spaces --bg 1

mri_glmfit command line I used: mri_glmfit --y lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.mgh --fsgd fsgd.txt dods --glmdir lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir --surf fsaverage lh --C group.diff.mtx --C group-x-age.mtx --C group-x-SA.mtx --C group-x-IQ.mtx --C lgi.intercept.mtx --C maineffect.age.mtx --C maineffect.IQ.mtx --cortex --eres-save

Also, is it okay to run the --eres-save flag with mri_glmfit regardless even if I decide to do another correction (i.e. monte carlo later later on) or would results get affected?

Thank you so much for your support,

Avi

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