[Freesurfer] Question about mri_glmfit
*Hello,* *I would like to conduct an analysis using mri_glmfit but I'm getting this error:* *ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08* *I am appreciated you can help me solve this problem. * *My command was:* mri_glmfit --y age9vs8ml01.mgh --fsgd new.fsgd dods --C age9vs8mlmatrix.mtx --surf fsaverage lh --cortex --glmdir glmdir.age9vs8ml Design matrix -- 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 Thanks Jincheng. age9vs8m.fsgd Description: Binary data age9vs8mlmatrix.mtx Description: Binary data ___ Freesurfer mailing list 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.
Re: [Freesurfer] Question about mri_glmfit
Hi there, Anyone can help me out? Thank you. 2016-09-28 13:46 GMT-04:00 kinson li : > *Hello,* > > *I would like to conduct an analysis using mri_glmfit but I'm getting this > error:* > > *ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08* > > *I am appreciated you can help me solve this problem. * > > *My command was:* > > mri_glmfit --y age9vs8ml01.mgh --fsgd new.fsgd dods --C > age9vs8mlmatrix.mtx --surf fsaverage lh --cortex --glmdir glmdir.age9vs8ml > > > Design matrix -- > > 1.000 0.000 8.000 0.000; > > 1.000 0.000 8.000 0.000; > > 1.000 0.000 8.000 0.000; > > 1.000 0.000 8.000 0.000; > > 1.000 0.000 8.000 0.000; > > 1.000 0.000 8.000 0.000; > > 1.000 0.000 8.000 0.000; > > 1.000 0.000 8.000 0.000; > > 1.000 0.000 8.000 0.000; > > 1.000 0.000 8.000 0.000; > > 1.000 0.000 8.000 0.000; > > 1.000 0.000 8.000 0.000; > > 1.000 0.000 8.000 0.000; > > 1.000 0.000 8.000 0.000; > > 1.000 0.000 8.000 0.000; > > 1.000 0.000 8.000 0.000; > > 1.000 0.000 8.000 0.000; > > 1.000 0.000 8.000 0.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > 0.000 1.000 0.000 9.000; > > > > ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 > > > > > Thanks > > Jincheng. > > ___ Freesurfer mailing list 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.
Re: [Freesurfer] Question about mri_glmfit
Hi Greve Thanks for your reply, can I have more detail about how to solve my problem. By the way, I may not think it's the problem about covariates. Thank you. Jin 2016-09-28 15:29 GMT-04:00 Douglas Greve : > Try normalizing your covariates (ie, subtract the mean and divide by the > stddev). > > On 9/28/16 3:07 PM, kinson li wrote: > > Hi there, > > Anyone can help me out? Thank you. > > 2016-09-28 13:46 GMT-04:00 kinson li : > >> *Hello,* >> >> *I would like to conduct an analysis using mri_glmfit but I'm getting >> this error:* >> >> *ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08* >> >> *I am appreciated you can help me solve this problem. * >> >> *My command was:* >> >> mri_glmfit --y age9vs8ml01.mgh --fsgd new.fsgd dods --C >> age9vs8mlmatrix.mtx --surf fsaverage lh --cortex --glmdir glmdir.age9vs8ml >> >> >> Design matrix -- >> >> 1.000 0.000 8.000 0.000; >> >> 1.000 0.000 8.000 0.000; >> >> 1.000 0.000 8.000 0.000; >> >> 1.000 0.000 8.000 0.000; >> >> 1.000 0.000 8.000 0.000; >> >> 1.000 0.000 8.000 0.000; >> >> 1.000 0.000 8.000 0.000; >> >> 1.000 0.000 8.000 0.000; >> >> 1.000 0.000 8.000 0.000; >> >> 1.000 0.000 8.000 0.000; >> >> 1.000 0.000 8.000 0.000; >> >> 1.000 0.000 8.000 0.000; >> >> 1.000 0.000 8.000 0.000; >> >> 1.000 0.000 8.000 0.000; >> >> 1.000 0.000 8.000 0.000; >> >> 1.000 0.000 8.000 0.000; >> >> 1.000 0.000 8.000 0.000; >> >> 1.000 0.000 8.000 0.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> 0.000 1.000 0.000 9.000; >> >> >> >> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 >> >> >> >> >> Thanks >> >> Jincheng. >> >> > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > Freesurfer mailing list > 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 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.
Re: [Freesurfer] question about Unpaired T-test group analysis
Hi there, Is there anyone can answer my questions? Thank you. 2016-10-11 11:41 GMT-04:00 kinson li : > *Hello, * > > *Question 1: I would like to conduct an Unpaired T-test group analysis, I > have two group of people, Group A8 age is 8 and Group A9 age is 9, and I to > test the* change in thickness with age. But I am little confusion about > the matirx and FSGD design. I am appreciated if you can take a look at my > FSGD file and Matrix file. Please correct me if I am wrong, > > Question2 : I am using tksurfer to analysis the brain thickness, and I > have a question about setting threshold, for I am not so sure about the > relation between threshold and Min. > is the equation Min = -log10(threshold) correct?(https://surfer.nmr. > mgh.harvard.edu/fswiki/FsTutorial/Visualization) > For example, if I want the threshold to be 0.05, and the Min will be set > to 1.3 > Please see the image attached in this email, and correct me if I am wrong. > > Thank you! > > Jincheng > ___ Freesurfer mailing list 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.
