never mind! It turned out I was forgetting to run a script to move copies of the fixed fsgd files into their final locations. Once I did so the files I posted worked fine. Sorry for the false alarm and thanks for getting back to me!
Joe > On Mar 3, 2016, at 12:18, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > I cannot replicate the error. What version of FS are you using? What > happens if you run > mri_glmfit --fsgd RPA-acc.fsgd > or > mri_glmfit --fsgd RPA-accGT.fsgd > > > > On 02/29/2016 09:38 PM, Joseph Dien wrote: >> Hi, >> I’m having an fsgd error that has totally stumped me. I’m trying to run >> the following command to compute the second level statistics: >> >> mri_glmfit --surf fsaverage lh --y ces.nii.gz --wls cesvar.nii.gz --nii.gz >> --fsgd RPA-accGT.fsgd --glmdir conVinc_normAcc.wls --C main.mtx --C >> normAcc.mtx >> >> I get the error message: >> >> Reading source surface /Volumes/Data2/RP1/freesurfer/fsaverage/surf/lh.white >> gdfReadHeader: reading RPA-accGT.fsgd >> FSGDF Format Error: file = RPA-accGT.fsgd, tag=Title >> >> I used the utility flip to make sure the file was in UNIX format (with >> linefeeds). >> I then double-checked by reading in the binary codes with Matlab’s fread and >> directly checking the ASCII numbers, which are indeed ASCII 10 (linefeed). >> >> Here is the contents of the fsgd file. >> >> GroupDescriptorFile 1 >> Title RP1 >> Class Main >> Variables LogoAcc NormAcc OrthAcc PhonAcc >> Input RPA903 Main 0.75 0.79 0.77 0.62 >> Input RPA906 Main 0.81 0.81 0.83 0.74 >> Input RPA907 Main 0.87 1 0.84 0.83 >> Input RPA908 Main 0.91 0.93 0.95 0.89 >> Input RPA909 Main 0.74 0.95 0.72 0.72 >> Input RPA910 Main 0.85 0.96 0.81 0.79 >> Input RPA912 Main 0.75 0.78 0.73 0.73 >> Input RPA914 Main 0.7 0.85 0.83 0.81 >> Input RPA915 Main 0.85 0.89 0.75 0.83 >> Input RPA916 Main 0.84 0.92 0.87 0.72 >> Input RPA917 Main 0.83 0.93 0.92 0.83 >> Input RPA918 Main 0.87 0.91 0.79 0.85 >> Input RPA919 Main 0.86 0.96 0.91 0.88 >> Input RPA920 Main 0.84 0.92 0.87 0.84 >> Input RPA921 Main 0.87 0.92 0.88 0.85 >> Input RPA922 Main 0.8 0.9 0.9 0.72 >> >> What’s really driving me to distraction is that a previous version of this >> file (with a different set of participants) works fine. I’m attaching both. >> RPA-accGT.fsgd does not work and RPA-acc.fsgd does work. Using Matlab’s >> fread, the first 85 characters (first four lines) of both files are >> identical. >> >> I’m running on OS X 10.11.3. I’m using FSFAST 5.20. Matlab 2015b. >> >> Any help would be greatly appreciated! >> >> Joe >> >> >> >> -------------------------------------------------------------------------------- >> >> Joseph Dien, PhD >> Senior Research Scientist >> Maryland Neuroimaging Center >> University of Maryland, College Park >> E-mail: jdie...@mac.com >> Cell Phone: 202-297-8117 >> http://joedien.com >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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. -------------------------------------------------------------------------------- Joseph Dien, PhD Senior Research Scientist Maryland Neuroimaging Center University of Maryland, College Park E-mail: jdie...@mac.com Cell Phone: 202-297-8117 http://joedien.com
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