The file I looked at had a bunch of carriage returns (try looking at it with more or less or cat). As long as those are in there, it will create an error.
Try running this and using the new one cat g4v1.73.fsgd | sed 's/\r/\n/g' > new.g4v1.73.fsgd On 12/12/2014 12:09 PM, lindsay hanford wrote: > Hi Doug! > > Thank you very much for your reply. I made the fsgd file in a > plain-text file using the textedit program on a Mac and when that > didn't work I tried modifying in the terminal window using: nano -w > g4v1.73.fsgd. > This also didn't solve the problem. I am not sure what to try next. > > Lindsay > > On Thu, Dec 11, 2014 at 9:09 AM, lindsay hanford > <[email protected] <mailto:[email protected]>> wrote: > > Hello, > > Has anyone had a chance to look at this? I still haven't been able > to solve the problem. > Thanks! > > Lindsay > > On Mon, Dec 1, 2014 at 2:41 PM, lindsay hanford > <[email protected] <mailto:[email protected]>> wrote: > > Hello Freesurfer Experts! > > I am encountering the dreaded mri_glmfit error: matrix is > ill-conditioned or badly scaled, condno = 1e+08. I have tried > to troubleshoot how to solve this problem from other > inquiries, however, I still have had no luck. I am trying to > run a 4 group 1 variable analysis: with diagnosis being my > variable of interest and trying to regress out the effects of > sex and age. > > 1. Command line: > mri_glmfit --y lh.10.73.SZHC.mgh --fsgd g4v1.73.fsgd dods > --C SZ-HC.intercept.73.mtx --surf fsaverage lh --cortex > --glmdir g4v1.73.lh > 2. The FSGD file (if using one) (see attached) > 3. And the design matrix: > 0.5 0.5 -0.5 -0.5 0 0 0 0 (or see attached) > > To the best of my knowledge, all my files are the right format > and I believe I have adequate number of participants per group? > I also tried mean centering my age variable. I had success > when I ran just a two group analysis (diagnosis) not > controlling for sex or age, however, as soon as I try to run > four groups, I encounter this error. I have no idea how to > proceed. > > I am looking forward to your response! > Thanks, > > > Lindsay > > -- > Lindsay Hanford, BSc, PhD Candidate > McMaster Integrative Neuroscience Discovery & Study| > *Department of Psychology, Neuroscience & Behaviour * > McMaster University *|* 1280 Main Street West, PC329 > Psychology Building *|* Hamilton, ON, L8S 4L8 > 905 525 9140 x24784 > <tel:905%20525%209140%20x24784>***|*[email protected] > <mailto:[email protected]> > > > > > -- > Lindsay Hanford, BSc, PhD Candidate > McMaster Integrative Neuroscience Discovery & Study| *Department of > Psychology, Neuroscience & Behaviour * > McMaster University *|* 1280 Main Street West, PC329 Psychology > Building *|* Hamilton, ON, L8S 4L8 > 905 525 9140 x24784***|*[email protected] > <mailto:[email protected]> > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list [email protected] 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.
