External Email - Use Caution Thank you for your reply! Using DOSS is precisely what I was trying to do, but mri_glmfit doesn't let me. I worked around by creating the design matrix in matlab and specify it to mri_glmfit directly, but I was wondering whether this might be bug in the parsing of the FSGD file. As a minimal example to reproduce, see the attached file. Trying to run mri_glmfit (doesn't even need more input specified), I get:
$ mri_glmfit --fsgd dosstest.fsgd doss
gdfRead(): reading dosstest.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 C 32.1111 8.50417
1 D 0.555556 0.496904
2 E 5.44444 3.49956
Class Size and Means of each Continuous Variable
1 A 1 50.0000 1.0000 4.0000
2 B 8 29.8750 0.5000 5.6250
ERROR: Class A has 1 members. With 3 variables and using DODS, you need at
least 4 members
dosstest.fsgd:
GroupDescriptorFile 1
Title DOSSTest
DOSS
Class A
Class B
Variables C D E
Input SUBJECT1 A 50 1 4
Input SUBJECT2 B 30 0 12
Input SUBJECT3 B 29 0 5
Input SUBJECT4 B 31 1 3
Input SUBJECT5 B 20 1 4
Input SUBJECT6 B 42 1 6
Input SUBJECT7 B 33 0 11
Input SUBJECT8 B 30 0 1
Input SUBJECT9 B 24 1 3
Concerning demeaning: I am only going to use a contrast vector for differences
in intercept between the groups [-1 1 0 0 0] and had the understanding that
demeaning would't be necessary in this case. Am I mistaken or is there other
reasons to do this especially for eTIV?
Thank you very much and
with best wishes,
Cornelius
> Date: Fri, 9 Jul 2021 14:05:31 -0400
> From: "Douglas N. Greve" <dgr...@mgh.harvard.edu>
> Subject: Re: [Freesurfer] mri_glmfit DOSS
>
> 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://secure-web.cisco.com/1pPOfqP7ALbHwAeCTJZowgLS8JJNUeA6-Z2RJlgx_6oCnQF0gABWOt_8KrLqoDdcjmbmoG9ym3ZtPvsAO1c68acEYJzrAsmFdzEWgPvb3kdwepaF35Hzwy4XTDhf8Mva0E4aHKtONsEKO44MeLe-FQDGn8hTUhVHWbd0M4oGtpgCfj_my9jlt9AoVNwgwNCyT4FImqIZy43WM2t69wzhU5ZyWyod4Pz_knEoEKB7FwqV3UX65_75Yv5PUJdpQmY_K9lKjYA0GH86Cv6X2Ru5JnQFHsGQgC0Rt3QRHIzfsrzg/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
> >
> >
dosstest.fsgd
Description: dosstest.fsgd
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