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Hi,Douglas,
Thanks for your reply! I have changed the classes and the contrast as
your suggestion. But I still met some problem when viewed the results. I still
met the problem when I loaded the sig.mgh file into freeview or qdec. I still
don't know how to see the result. Thank you in advance!
At 2020-02-21 06:00:57, "Douglas N. Greve" <dgr...@mgh.harvard.edu> wrote:
Don't use gender as a continuous variable. You need four classes (TLE-Male,
TLE-Female, etc) and change the contrast to reflect it, otherwise I think it
looks ok. Load the sig.mgh file into freeview (or the tksurferfv freeview
wrapper)
On 2/19/2020 10:31 PM, 邓刊 wrote:
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Dear Freesurfer support,
we met some probelm when we investigate difference between two groups. We
have two sets of data, one is the TLE group, the other is the extraTLE. We also
has the variables: age,gender and neuropsychological test scores. We want to
analyze the relationship between cortical thickness and neuropsychological
test, controlling for age, gender and group.
The contrast in the full DODS model in the mri_glmfit is 0 0 0 0 0.5 0.5 0
0, with the fsgd file being:
GroupDescriptorFile 1 Title MyTitle MeasurementName thickness Class Class1_TLE
Class Class3_extra_TLE Variables Age factor4 gender Input PT1_01 Class1_TLE 23
12 1 Input PT1_03 Class1_TLE 38 10.26 0 Input PT1_04 Class1_TLE 26 13 0 Input
PT1_06 Class1_TLE 45 13 1 Input PT1_11 Class1_TLE 20 15 1 Input PT1_12
Class1_TLE 23 10.26 0 Input PT1_14 Class1_TLE 39 9 1 Input PT1_27 Class1_TLE 51
14 1 Input PT1_32 Class1_TLE 33 11 0 Input PT1_33 Class1_TLE 27 8 1 Input
PT1_34 Class1_TLE 19 8 0
Preproc was done with:
mris_preproc --fsgd patients_age_gender_Arithmetic.fsgd \
--cache-in thickness.fwhm15.fsaverage \
--target fsaverage \
--hemi rh \
--out rh_thickness_Arithmetic/rh.thickness.fwhm15_arithmetic.mgh
GLM was done with:
mri_glmfit --y rh_thickness_Arithmetic/rh.thickness.fwhm15_arithmetic.mgh \
--fsgd patients_age_gender_Arithmetic.fsgd dods \
--C difference_Arithmetic_all.mtx \
--surf fsaverage rh \
--glmdir rh_thickness_Arithmetic
My questions are：
(1)Are the command lines, fsgd file and the contrast matrix correct?
(2)We have used qdec (DODS) to visualize the results, but I can't open the
sig.mgh file. I dont know why? The terminal shows that :
Reading /usr/local/freesurfer/tktools/tkUtils.tcl
Using /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl
ERROR: MRISread: file
'/usr/local/freesurfer/subjects/Neuropsychology/rh_thickness_Arithmetic/difference_Arithmetic_all/F.mgh'
has 0 vertices!
Probably trying to use a scalar data file as a surface!
Invalid argument
I dont know how to solve it. I very appreciate your help.
Kind regards,
Kan
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