Oops, never mind. User error. I’m too embarrassed to even explain what I did. :)
Joe
On Feb 29, 2016, at 21:38, Joseph Dien jdien07@mac.com 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
<RPA-accGT.fsgd><RPA-acc.fsgd>
Joseph Dien, PhD Senior Research Scientist Maryland Neuroimaging Center University of Maryland, College Park E-mail: jdien07@mac.com Cell Phone: 202-297-8117 http://joedien.com
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Joseph Dien, PhD Senior Research Scientist Maryland Neuroimaging Center University of Maryland, College Park E-mail: jdien07@mac.com Cell Phone: 202-297-8117 http://joedien.com