you can still use contrasts.sig.mgh, I just don't know what the order
is. You can run mri_segstats on the sig.mgh files from the individual
contrasts, with either --avgwf or --sum, either way works.
On 8/24/2020 12:32 PM, Rizvi, Batool wrote:
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 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
The information in this e-mail is intended only for the person to whom
it is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you
in error
but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
