External Email - Use Caution
Thanks Dr. Greve, I'll CC the FS support team this time as well.
That's correct, I got the contrasts.sig.mgh file from QDEC.
So in order to get the p-values of each of the associations (for ex: age and
cortical thinning), which command and input file should I use? Would it still
be the mri_segstats command, but without the --avgwf option?
Thanks again for your help and time!
Batool
From: Douglas N. Greve <dgr...@mgh.harvard.edu>
Sent: Monday, August 24, 2020 10:11 AM
To: Rizvi, Batool <br2...@cumc.columbia.edu>; Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] extracting beta coefficients and p-values
answers below. also, please remember to post to the list
On 8/21/2020 6:52 PM, Rizvi, Batool wrote:
External Email - Use Caution
Thank you Dr. Greve! This is very helpful! Just to confirm, similar to taking
the effect of age, if I wanted to get the beta of Parietal WMH (my main
continuous IV), I would just average betas 5-8?
I forgot to add this in my previous email, but I'm also trying to extract
p-values of all the variables involved, and wasn't sure how to. I tried running
a couple different commands.
When I ran this below command, I got a file with 1 column of 8 numbers:
mri_segstats --i contrasts.sig.mgh --annot fsaverage lh
lh-Avg-long.thickness-spc-Parietal_WMH-Cor/mc-z.abs.th20.sig.ocn.annot
--excludeid 0 --avgwf avgwfsig.dat
where did contrasts.sig.mgh come from? Was this created by QDEC?
But when I tried the below command, I got a file with 1 number.
mri_segstats --i lh-Avg-long.thickness-spc-Parietal_WMH-Cor/sig.mgh --annot
fsaverage lh
lh-Avg-long.thickness-spc-Parietal_WMH-Cor/mc-z.abs.th20.sig.ocn.annot
--excludeid 0 --avgwf avgwfsig2.dat
>From the 1st way (using contrasts.sig.mgh):
-0.27711
-2.51072
0.42697
0.62922
-0.85069
0.52623
1.00393
-0.42921
>From the 2nd way (using sig.mgh)
-2.51072
I'm pasting my fsgd format once more:
GroupDescriptorFile 1
Title ParietalWMH_age_gender_APOe_EC_left
MeasurementName long.thickness-spc
Class APOE_statusNO-genderF
Class APOE_statusYES-genderF
Class APOE_statusNO-genderM
Class APOE_statusYES-genderM
Variables Parietal_WMH age_years Avg_ECthickness
Input W38284_base APOE_statusNO-genderF 0.732010 85.830000 3.125000
.. (only listing the 1st Input line here)
My contrast file (C.dat) looks like below:
0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0
And I'm trying to find p-values for these variables' associations w/ thickness:
APOE status, gender, Parietal WMH, Age, Avg EC thickness.
Each contrast will have a sig file. But the command above will compute the
average significance, which really does not mean anything
Thanks so much again for all the help!
Batool
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