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 1^st way (using contrasts.sig.mgh):
-0.27711
-2.51072
0.42697
0.62922
-0.85069
0.52623
1.00393
-0.42921
From the 2^nd 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 1^st 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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
