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Dear all,
this error seems to be gdfCheckNPerClass in utils/fsgdf.cpp. Using "doss" or
"DOSS" as a tag in the FSGD file doesn't help either, strangely. Could it be
that it should be strcasecmp() instead of strcmp() in line 1046 of fsgdf.cpp?
Cheers,
Cornelius
Date: Tue, 29 Jun 2021 15:19:20 +0000
From: "Dr. Cornelius Kronlage"
<cornelius.kronl...@med.uni-tuebingen.de>
Subject: [Freesurfer] mri_glmfit DOSS
To: "'freesurfer@nmr.mgh.harvard.edu'"
<freesurfer@nmr.mgh.harvard.edu>
Message-ID: <2a173629cd4540769ec6a07d892ca...@med.uni-tuebingen.de>
Content-Type: text/plain; charset="us-ascii"
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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-FObJ8JCIIzwnlckPdClcabJkNNzasGdp_baoY3vFivUVTYKJkWgkuc4zGLEuruJqTFJupPLGS1I-n-IqrMT71wsYNjafciK0No5U2Ht7uG3R-qFReinEp_MecJ9YmfIFhW0ziWBvX_nknV20c9cIGk7hfeC2raoWWBVBbBw6-fQ_YasVd7Tv4WOYVgHcneMGz-jBtgcojHACBL4ql-DTGUQtWydFrpa2B2CXNbzOyFKzQJNEgklSCSyEgY8q0aHfg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdExamples
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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