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If I have 4 groups GroupDescriptorFile 1 Title XXX Class G1 Class G2 Class G3 Class G4 Input subj1 G1 Input subj2 G3 Input subj3 G2 Input subj4 G2 Input subj5 G4 .... Are the contrasts below corrected? G1_only_thick 1 0 0 0 G2_only_thick 1 0 0 0 G3_only_thick 1 0 0 0 G4_only_thick 1 0 0 0 G1+G2-G3+G4_thick 0.5 0.5 -0.5 -0.5 G3+G4+G2+G1_thick -0.5 -0.5 0.5 0.5 G1+G2+G3+G4_thick 0.25 0.25 0.25 0.25 Thanks Stefano Yes, you use a "per-vertex map" (--pvr option to mri_glmfit). See, example, this thread https://secure-web.cisco.com/1951sWOE8h4m5NbLCNqMyCAH8IOXE-lQF7pVtK2O9WlGr4lhC_ZayJW3oVHincxLs53lKvn0Z-ft-svmipnYED9p-xyQou2z1oP685gnJy3DM4X5tON-4zkvd1sP1xWnF1nZd9lZy-XdrKD8EufxxsG-gOreUvYzG0cA8pE1W8jkaYloEpe1annxnW8XXl-kmnIHZf1--oFrTvMN64dAA6I2FO5CoCq1z-DrzvgSl3fP4l15sZISoKwYj68dddQJm69YYEODA7eKQ5rzp3VtndQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg18790.htmlOn 6/3/2021 10:22 AM, std...@virgilio.it mailto:std...@virgilio.it wrote: > External Email - Use Caution Hi, how can I perform vertex by vertex (surface) > analysis of covariance between functional connectivity data (FS-FAST) and > cortical thickness, regressing out the effect of groups?My mean concern is > how buid the fsgd file. Stefano > Great news, thank you, Doug! Best, aga On 8/3/11 5:02 PM, Douglas N Greve mailto:gr...@nmr.mgh.harvard.edu wrote: >Hi Aga, what you have done is correct, no need to include the pvr in the >fsgd. >doug > >Burzynska, Aga wrote: >> Dear all, >> I am trying to make group level analysis of functional data on the >>surface and add per-vertex regressors (PVR, here: cortical thickness) >>into the design. When I view the results I have the feeling that the PVR >>is not really included in the model: >> >> I am using the command: >> mri_glmfit --glmdir lh_output --y cope1_lh_4D.mgh --fsgd >>Group1versusGroup2.fsgd --pvr lh.thickness.10.mgh --C >>Group1only_thickness.mat --C Group2only_thickness.mat --C >>Group1minusGroup2_thickness.mat --C Group2minusGroup1_thickness.mat --C >>Group1plusGroup2_thickness.mat >> >> where >> cope1_lh_4D.mgh contains the concatenated sig.mgh images from the fixed >>level analysis (combining the runs) for each participant >> fsgd file contains: >> GroupDescriptorFile 1 >> Title Group1versusGroup2 >> Class Group1 >> Class Group2 >> Input 1109 Group1 >> Input 1110 Group1 >> Input 1111 Group1 >> Input 1112 Group1 >> ... >> Input 2280 Group2 >> Input 2282 Group2 >> Input 2283 Group2 >> Input 2284 Group2 >> >> The PVR is a file containing thickness maps for each participant, >>concatenated in the same order as for the functional data. >> >> So there are 2 main regressors (1 factor, 2 levels), but the contrast >>files contain 3 regressors (the third one is the PVE), for instance: >> Group1minusGroup2_thickness.mat contains 1 -1 0. >> >> Does it look correct? >> Should the pvr regressor be included in the fsdg file? How can I do it? >> >> Thank you very much for your help, >> Cheers, >> Aga >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> https://secure-web.cisco.com/1j7gX2AgIkSf91OBjYTSReZHX2EetZX7rsmwgY8OFEwb24dVG__03Lc8oV1p9AmN6j1NH56r3VFWCJbm4hxC2VDJszNqjomarUeeVEy9EcpEKqXBME-7bmuYqrr9SBpd-ejzmfSpM-qXGknGPGvi4mR8L36y5CEX3hRXJbuoSjbDOp2O3jyu5BCxn9rjs6X4gGeisP83uTiXbzC36BLA7D3wx_m-FaovrOJKB7ubNxHETJ12Nj8CXi6tDJ96p_nQ7UmRxEJqDj_aV30OTYMVMMg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> >> >> > >-- >Douglas N. 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