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

 

answers below. also, please remember to post to the list

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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

 

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