Am I correct in assuming this results in z-scoring/normalizing the covariates?
Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging > On Oct 28, 2019, at 7:33 AM, Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu> > wrote: > > My guess is that your covariates have almost no range to them and so look > like constant (similar to columns 1 and 2). You can try demeaning and > rescaling the covariates. You can do this by hand and create a new FSGD file > or you can add the following lines anywhere in the fsgd: > RescaleFlag 1 > DemeanFlag 1 > > > On 10/26/19 10:45 PM, Nillo, Ryan Michael R wrote: >> Hello, >> >> I ran mri_glmfit with the following fsgd file: >> >> GroupDescriptorFile 1 >> Title CJD >> >> Class MM1_MV1 >> Class MV2_VV2 >> >> Variables frontal >> >> Input 7693 >> MV2_VV2 2.930667 >> Input 11985 >> MV2_VV2 2.410333 >> Input 13082 >> MV2_VV2 2.529333 >> Input 13425 >> MV2_VV2 2.593667 >> Input 13667 >> MM1_MV1 2.628667 >> Input 13900 >> MM1_MV1 2.675333 >> Input 14094 >> MM1_MV1 2.549333 >> Input 15566 >> MV2_VV2 2.666667 >> Input 15999 >> MM1_MV1 2.641 >> Input 16714 >> MV2_VV2 2.643 >> Input 16848 >> MV2_VV2 2.63 >> Input 16952 >> MV2_VV2 2.516 >> Input 7693a >> MV2_VV2 3.054 >> Input 11985a >> MV2_VV2 2.42 >> Input 13082a >> MV2_VV2 2.454 >> Input 13425a >> MV2_VV2 2.602 >> Input 13667a >> MM1_MV1 2.604333 >> Input 13900a >> MM1_MV1 2.601333 >> Input 14094a >> MM1_MV1 2.523333 >> Input 15566a >> MV2_VV2 2.713333 >> Input 15999a >> MM1_MV1 2.584333 >> Input 16714a >> MV2_VV2 2.673333 >> Input 16848a >> MV2_VV2 2.533333 >> Input 16952a >> MV2_VV2 2.486 >> >> My two contrast matrices are: >> one.mtx = [ 0 0 1 0 ] >> two.mtx = [ 0 0 0 1 ] >> >> When running the mri_glmfit command "mri_glmfit --glmdir new.frontal.lgi >> --fsgd new.frontal.fsgd.txt --fwhm 30 --surf fsaverage lh --y >> lh.pial_lgi.fwhm0.mgh --C one.mtx --C two.mtx”, I get the following output: >> >> INFO: gd2mtx_method is dods >> Saving design matrix to new.frontal.lgi/Xg.dat >> Computing normalized matrix >> Normalized matrix condition is 12820.7 >> Design matrix ------------------ >> 0.00000 1.00000 0.00000 2.93067; >> 0.00000 1.00000 0.00000 2.41033; >> 0.00000 1.00000 0.00000 2.52933; >> 0.00000 1.00000 0.00000 2.59367; >> 1.00000 0.00000 2.62867 0.00000; >> 1.00000 0.00000 2.67533 0.00000; >> 1.00000 0.00000 2.54933 0.00000; >> 0.00000 1.00000 0.00000 2.66667; >> 1.00000 0.00000 2.64100 0.00000; >> 0.00000 1.00000 0.00000 2.64300; >> 0.00000 1.00000 0.00000 2.63000; >> 0.00000 1.00000 0.00000 2.51600; >> 0.00000 1.00000 0.00000 3.05400; >> 0.00000 1.00000 0.00000 2.42000; >> 0.00000 1.00000 0.00000 2.45400; >> 0.00000 1.00000 0.00000 2.60200; >> 1.00000 0.00000 2.60433 0.00000; >> 1.00000 0.00000 2.60133 0.00000; >> 1.00000 0.00000 2.52333 0.00000; >> 0.00000 1.00000 0.00000 2.71333; >> 1.00000 0.00000 2.58433 0.00000; >> 0.00000 1.00000 0.00000 2.67333; >> 0.00000 1.00000 0.00000 2.53333; >> 0.00000 1.00000 0.00000 2.48600; >> -------------------------------- >> ERROR: matrix is ill-conditioned or badly scaled, condno = 12820.7 >> -------------------------------- >> Possible problem with experimental design: >> Check for duplicate entries and/or lack of range of >> continuous variables within a class. >> If you seek help with this problem, make sure to send: >> 1. Your command line: >> mri_glmfit --glmdir new.frontal.lgi --fsgd new.frontal.fsgd.txt --fwhm >> 30 --surf fsaverage lh --y lh.pial_lgi.fwhm0.mgh --C one.mtx --C two.mtx >> 2. The FSGD file (if using one) >> 3. And the design matrix above >> Attempting to diagnose further >> SumSq: Min=2.828427 (col 1), Max=10.485683 (col 4) >> ... could not determine the cause of the problem >> >> >> Can anyone give me some insight into what might be going wrong? >> >> Thanks so much, >> >> Ryan Michael Nillo >> Staff Research Associate I >> University of California San Francisco >> Department of Radiology and Biomedical Imaging >> >> >> >> External Email - Use Caution >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwMGaQ&c=iORugZls2LlYyCAZRB3XLg&r=-dSNp2WfY7DySdV4_Sqc4m6hoXOmD3OskcWVyhGbe1U&m=vKhgpt5PEzT-yI2H0mxJSvVsVu8umLM48iQq3tLnYSo&s=3T7IJN0p7_TTHTPG05lWEjp2P2IbHoD4ZHnsVQn7_OE&e=> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwICAg&c=iORugZls2LlYyCAZRB3XLg&r=-dSNp2WfY7DySdV4_Sqc4m6hoXOmD3OskcWVyhGbe1U&m=vKhgpt5PEzT-yI2H0mxJSvVsVu8umLM48iQq3tLnYSo&s=3T7IJN0p7_TTHTPG05lWEjp2P2IbHoD4ZHnsVQn7_OE&e=
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