Yes On 10/28/19 1:04 PM, Nillo, Ryan Michael R wrote: > 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 <mailto: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 >>> >>> Variablesfrontal >>> >>> Input7693MV2_VV22.930667 >>> Input11985MV2_VV22.410333 >>> Input13082MV2_VV22.529333 >>> Input13425MV2_VV22.593667 >>> Input13667MM1_MV12.628667 >>> Input13900MM1_MV12.675333 >>> Input14094MM1_MV12.549333 >>> Input15566MV2_VV22.666667 >>> Input15999MM1_MV12.641 >>> Input16714MV2_VV22.643 >>> Input16848MV2_VV22.63 >>> Input16952MV2_VV22.516 >>> Input7693aMV2_VV23.054 >>> Input11985aMV2_VV22.42 >>> Input13082aMV2_VV22.454 >>> Input13425aMV2_VV22.602 >>> Input13667aMM1_MV12.604333 >>> Input13900aMM1_MV12.601333 >>> Input14094aMM1_MV12.523333 >>> Input15566aMV2_VV22.713333 >>> Input15999aMM1_MV12.584333 >>> Input16714aMV2_VV22.673333 >>> Input16848aMV2_VV22.533333 >>> Input16952aMV2_VV22.486 >>> >>> 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 >>> *MailScanner has detected a possible fraud attempt from >>> "urldefense.proofpoint.com" claiming to be* >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto: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= >> >> > > > External Email - Use Caution > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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