Are you loading the one created by mri_glmfit (in the output directory)?

doug

On Mon, 6 Apr 2009, Jeff Sadino wrote:

Thank you for the advice Sid. I added those lines, and now my errors disappear, but I still get a blank screen where there should be a scatterplot. Is this a graphics issue with my hardware, or do I need to do something differently?

This is my fsgd file: GroupDescriptorFile 1 Title try1 MeasurementName thickness Class nc circle red Variables Age Input 060017_HG01 nc .5 Input 060023_F01 nc .8 Input 060024_HG01 nc .1 Input 060025_HG01 nc .5 ... ...

The screen that pops up has thickness on the y-axis, but a range of only 0-1 and Age on x-axis with range 0-1. My ages were "real" (50.8, 40.8, 50.1, etc.), but I changed them to between 0 and 1 to see if that helped, but no good.

Thanks in advance for your help, Jeff Sadino

Date: Thu, 12 Mar 2009 18:52:45 -0700 Subject: Re: [Freesurfer] tksurfer Load Group Descriptor File error From: siddys@gmail.com To: jsadino@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu

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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