External Email - Use Caution
Dear freesurfers,
for a morphometry study, I am comparing a single subject at a time to a group of controls. I would like to include age, gender (as a continuous variable for the sake of simplicity) and eTIV as "nuisance" regressors in the GLM. The FSGD looks like this:
GroupDescriptorFile 1 Title SUBJECT1_vs_allControls Class Test Class Controls Variables Age Gender eTIV Input SUBJECT1 Test 50 1 1497422.2500 Input SUBJECT2 Controls 30 0 1709039.536815 Input SUBJECT3 Controls 29 0 1423097.816203 Input SUBJECT4 Controls 31 1 1524690.026713 ...
When I try to run mri_glmfit I get the following error even though I specify DOSS:
$ mri_glmfit --fsgd SUBJECT1_vs_allControls.fsgd doss [...] gdfRead(): reading SUBJECT1_vs_allControls.fsgd WARNING: variable 1 is "Gender" which is often a discrete factor The proper way to handle discrete factors is to create classes. See https://secure-web.cisco.com/10ThHTirv10OEqbkasMHR-FObJ8JCIIzwnlckPdClcabJkN... INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 28.6875 6.36611 1 Gender 0.46875 0.499022 2 eTIV 1.51444e+06 125811 Class Size and Means of each Continuous Variable 1 Test 1 50.0000 1.0000 1497422.2500 2 Controls 31 28.0000 0.4516 1514993.8589 ERROR: Class Test has 1 members. With 3 variables and using DODS, you need at least 4 members How do I get mri_glmfit to use DOSS, or do I have to specify the design matrix by hand in this case?
Thank you! Best wishes Cornelius
You cannot use a DODS in this design as it tries to fit an offset and a slope for each class, which can't be done when the class has only one member. Try using DOSS instead. You should probably demean and rescale the eTIV to be between 0 and 1.
On 6/29/2021 11:19 AM, Dr. Cornelius Kronlage wrote:
External Email - Use Caution
Dear freesurfers,
for a morphometry study, I am comparing a single subject at a time to a group of controls. I would like to include age, gender (as a continuous variable for the sake of simplicity) and eTIV as “nuisance” regressors in the GLM. The FSGD looks like this:
GroupDescriptorFile 1 Title SUBJECT1_vs_allControls Class Test Class Controls Variables Age Gender eTIV
Input SUBJECT1 Test 50 1 1497422.2500 Input SUBJECT2 Controls 30 0 1709039.536815 Input SUBJECT3 Controls 29 0 1423097.816203 Input SUBJECT4 Controls 31 1 1524690.026713 ...
When I try to run mri_glmfit I get the following error even though I specify DOSS:
$ mri_glmfit --fsgd SUBJECT1_vs_allControls.fsgd doss [...]
gdfRead(): reading SUBJECT1_vs_allControls.fsgd WARNING: variable 1 is "Gender" which is often a discrete factor The proper way to handle discrete factors is to create classes. See https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 28.6875 6.36611 1 Gender 0.46875 0.499022 2 eTIV 1.51444e+06 125811 Class Size and Means of each Continuous Variable 1 Test 1 50.0000 1.0000 1497422.2500 2 Controls 31 28.0000 0.4516 1514993.8589 ERROR: Class Test has 1 members. With 3 variables and using DODS, you need at least 4 members
How do I get mri_glmfit to use DOSS, or do I have to specify the design matrix by hand in this case?
Thank you!
Best wishes Cornelius
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Douglas N. Greve -
Dr. Cornelius Kronlage