External Email - Use Caution
Thank you for getting back to me. You are correct in your in that the contrast
is C = (INT2-INT1)-(CON2-CON1). The measure of interest is SPC.
For the complete test we are trying to determine between group differences in
cortical thickness, adjusting for covariates (age, sex, and MoCA). I was
hoping to visualize this difference graphically using the
cache.th13.abs.y.ocn.dat file output.
This is our FSGD:
GroupDescriptorFile 1
Title Between-group
Class int_male
Class int_female
Class con_male
Class con_female
Variables age moca
Input 001.MR int_male 30 25
Input 002.MR int_female 40 22
Input 003.MR con_male 60 29
Input 004.MR con_female 60 21
…
And this is the contrast matrix
+0.5 +0.5 -0.5 -0.5 +0 +0 +0 +0 +0 +0 +0 +0
Thank you,
Ryan G. Stein
MSc Student, Rehabilitation Sciences
Aging, Mobility, and Cognitive Health Lab
Djavad Mowafaghian Centre for Brain Health
University of British Columbia | Vancouver Campus | Musqueam Traditional
Territory
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
Sent: August 28, 2022 12:45:22 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Group Analysis - glmfit results
[CAUTION: Non-UBC Email]
Since this is longitudinal, I'm assuming that your contrast is actually
something like contrast C = (INT2-INT1)-(CON2-CON1) where 1 and 2 the the time
points. As you suggest, both (INT2-INT1) and (CON2-CON1) might both be less
than 0, but if INT is less negative than CON, then C will be positive and
everything is working as it should (ie, there is not a problem or discrepancy
here). What is the (complete) test that you are trying to accomplish?
On 8/23/2022 3:10 PM, rstei...@student.ubc.ca<mailto:rstei...@student.ubc.ca>
wrote:
External Email - Use Caution
Hello Freesurfer Team,
I recently ran analysis to compare change in cortical thickness between an
Intervention and Control group longitudinally. The contrast is set up as
INT-CON, and therefore I would interpret a positive change as the intervention
having a greater increase in cortical thickness or less atrophy than the
control group.
The cluster that survived the Monte-Carlo simulation showed a positive
difference in the LH superior parietal region when running both an ‘abs’ and
‘pos’ simulation (these showed the same cluster.summary outputs). There was not
a significant cluster when running the ‘neg’ simulation. When I compared the
mean change in thickness between groups (cache.th13.abs.y.ocn.dat file), it
showed that the control group experienced less atrophy than the intervention
despite having a positive cluster output.
One possible solution I considered is accounting for baseline differences
between groups when looking at mean change. Does glmfit control for baseline
cortical thickness in the cluster analysis that is not accounted for in the
mean change values from the cache.th13.abs.y.ocn.dat file? Is there another
possible explanation for this discrepancy?
Thank you in advance,
Ryan S
Ryan G. Stein
MSc Student, Rehabilitation Sciences
Aging, Mobility, and Cognitive Health Lab
Djavad Mowafaghian Centre for Brain Health
University of British Columbia | Vancouver Campus | Musqueam Traditional
Territory
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://secure-web.cisco.com/1L-QUX0oxYF35oXaocuGgirTIOC1fHoZ7vjHDMwqY0H3zDfrv0N3j0uuS2nWFROUna_-FFELqB-Le8yNoB2E8XSFfOaweFdHpFQKuEezy4iGYk2zElYqGWlGmiEm34J7LMoXbtQpspU3YeAIZsMM04LfbdMmnpixQW2_oz17nOnHQUKf1s8J1pLnRaJXZeCs_hNFbcMQfO53VQRH_afdu5yJYv4vsunDfQk5k2BI4IGk4rQ6XQ2dJbL8f-pHybEVZJOxJu-OSdH9RHREYuaEf7yrlSgcWVEQsrgfn3JPvhZ6Jvl1sGx9um_AbkhBejSf5_qO4jfz3jICOUf38a5I8Vw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
