Class ctrl should be followed by marker and color specification (Class ctrl circle red, for e.g). ditto for cd .
sid.
On Thu, Mar 12, 2009 at 6:37 PM, Jeff Sadino jsadino@hotmail.com wrote:
Hello,
Can someone help me get scatterplots of my data? I am using freesurfer 3.0.5. I have ran these commands:
mris_preproc --fsgd try1.fsgd --target fsaverage --hemi lh --meas thickness --out lh.try1.mgh mri_surf2surf --hemi lh --s fsaverage --sval lh.try1.mgh --fwhm 10 --tval lh.try1.fw.mgh mri_glmfit --y lh.try1.fw.mgh --fsgd try1.fsgd dods --C try1.mtx --surf fsaverage lh --glmdir lh.try1.dir tksurfer fsaverage lh inflated -annot aparc.atlas2005_simple -overlay lh.try1.dir/try1.mtx/sig.mgh
Then selected a vertex, then File->Load Group Descriptor File and selected try1.fsgd, but I get this error:
WARNING: Marker for class ctrl was invalid. WARNING: Color for class ctrl was invalid. WARNING: Marker for class cd was invalid. WARNING: Color for class cd was invalid.
This is try1.fsgd:
GroupDescriptorFile 1 Title try1 MeasurementName thickness Class ctrl Class cd Variables Age Input 040004_P02 ctrl 55.18 Input 050046_S02 ctrl 37.45 ... ... Input 070073_S01 cd 20.54 Input 070114_OGM01 cd 46.03
I also tried with lh.try1.dir/y.fsgd, but get a similar error:
INFO: ignoring tag Creator INFO: ignoring tag SUBJECTS_DIR INFO: ignoring tag SynthSeed INFO: gdfRead: reshaping WARNING: Marker for class ctrl was invalid. WARNING: Color for class ctrl was invalid. WARNING: Marker for class cd was invalid. WARNING: Color for class cd was invalid.
y.fsgd looks like this:
GroupDescriptorFile 1 Title try1 MeasurementName external Tessellation surface PlotFile /data/Jeff/glmtut/pass5/try1/lh.try1.fw.mgh DesignMatFile fsgd.X.mat dods ResidualFWHM 22.331472 Class ctrl Class cd Variables Age Input 040004_P02 ctrl 55.18 Input 050046_S02 ctrl 37.45 ... ... Input 070073_S01 cd 20.54 Input 070114_OGM01 cd 46.03 Creator mri_glmfit SUBJECTS_DIR /share/apps/freesurfer/subjects SynthSeed 1237057379
In both cases, a graph pops up, but it is blank. Thank you in advance for your suggestions, Jeff Sadino
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