Can't tell without the fsgd file
On 3/7/2022 8:30 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
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Just to double check the numbers - I seem to have been getting into an
error in how many columns in the FSGD it is expecting.
I have 9 different sites, 4 different patient groups, and M/F -> 72
classes.
I also am covarying for four different factors, so the contrast matrix
I am making is 72*(4+1) long. Since I want to regress out the four
factors completely, only the first 72 numbers in 360 contrast matters.
My FSGD file has 4 columns e.g like
Input GP0001 NCBostonM 60 12000 -0.01 -0.02
It says ERROR: gdfReadV1: Input line 1, subjid = GP0001
Found 4 variables, expected. 10
Where is this 10 coming from?
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*From:* Zeng,Victor (BIDMC - Keshavan - Psychiatry)
<vz...@bidmc.harvard.edu>
*Sent:* Monday, February 21, 2022 5:50:46 PM
*To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [External] Re: [Freesurfer] classes for GLM analysis
Do you have a Freesurfer page I can read up on those hybrid ways just
to see whether that could be an option?
Also, although its a binary, you would recommend against have sex be a
continuous measurement like age, due to the design of how the
contrasts are determined? I.e continuous measurements aren't treated
like integers
Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--
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*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
*Sent:* Sunday, February 13, 2022 12:24 PM
*To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Subject:* [External] Re: [Freesurfer] classes for GLM analysis
It is probably not going to work very well if you have some classes
that only have one member. You can eliminate members of classes that
only have a few members. If you really need to have those cases, there
are hybrid ways to analyze the data (but you can't use an FSGD at that
point)
On 2/6/2022 10:41 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
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Hi all,
I am doing an analysis and generating the FSGD. I understand sex and
race are classes in this context, but something I was also hoping to
regress out is the effects of scanner/sequences. We have a large
participant size, so we have around 10+ scanner/sequences, which
makes for a large amount of classes combinations, with some having
just 1 (if not zero) fitting into a class.
Would you proceed with this nonetheless? If not, should
scanner/sequence be something that we consider? Should we find some
other way to adjust site (I don't think we can z-score...). Or can we
consider site/scanner as a continuous variable
Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
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