why are you using such an old version of freesurfer? If you have
subjects analyzed in 3.0.5 and don't want to re-run them in 4, you can
still do the group analysis in 4.
Jeff Sadino 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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