Hello!
I am trying to generate significance maps for a paired-difference analysis of cortical thickness using multiple pairs of siblings, and was wondering if there is a way to incorporate the family ID as a random effect/covariate in Freesurfer. Is it possible for the family ID for each sibling pair to be used as a categorical/discrete variable to then see the effect of family on cortical thickness in addition to the main effects we are looking at? Any guidance would be greatly appreciated!
Best, Casey
--
Casey Hopkinson
Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Massachusetts General Hospital 149 13th Street, Charlestown, MA, 02129 (p) 617.643.3215
I'm not sure I understand. Can you elaborate?
On 8/19/19 2:43 PM, Hopkinson, Casey E wrote:
Hello!
I am trying to generate significance maps for a paired-difference analysis of cortical thickness using multiple pairs of siblings, and was wondering if there is a way to incorporate the family ID as a random effect/covariate in Freesurfer. Is it possible for the family ID for each sibling pair to be used as a categorical/discrete variable to then see the effect of family on cortical thickness in addition to the main effects we are looking at? Any guidance would be greatly appreciated!
Best, Casey
*--*
*Casey Hopkinson*
Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Massachusetts General Hospital 149 13th Street, Charlestown, MA, 02129 (p) 617.643.3215
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Sure! We have been conducting analyses in a large sample of pairs of siblings to see the effect of prenatal exposures on cortical thickness. For the current analysis, we're looking at the effect of the exposure load (total # of exposures) on cortical thickness using a paired-difference model, so the covariant being used is the difference in exposure load between each pair. We're trying to figure out if it is possible to also covary for the family the siblings belong to (using the assigned Family ID), to see the effect of family on cortical thickness as well as exposure load. This was able to be done statistically, however we weren't sure if it could be done in Freesurfer, too.
My apologies if this is still unclear - please let me know if you have any further questions. Thank you!
Best, Casey
--
Casey Hopkinson
Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Massachusetts General Hospital 149 13th Street, Charlestown, MA, 02129 (p) 617.643.3215
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Monday, August 19, 2019 6:29 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Help with using family as random effect in sibling study
I'm not sure I understand. Can you elaborate?
On 8/19/19 2:43 PM, Hopkinson, Casey E wrote:
Hello!
I am trying to generate significance maps for a paired-difference analysis of cortical thickness using multiple pairs of siblings, and was wondering if there is a way to incorporate the family ID as a random effect/covariate in Freesurfer. Is it possible for the family ID for each sibling pair to be used as a categorical/discrete variable to then see the effect of family on cortical thickness in addition to the main effects we are looking at? Any guidance would be greatly appreciated!
Best, Casey
*--*
*Casey Hopkinson*
Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Massachusetts General Hospital 149 13th Street, Charlestown, MA, 02129 (p) 617.643.3215
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi everyone,
Just wanted to follow up with this in case anyone may have an idea of if this can be done. Thanks!
--
Casey Hopkinson
Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Massachusetts General Hospital 149 13th Street, Charlestown, MA, 02129 (p) 617.643.3215
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Hopkinson, Casey E CHOPKINSON@mgh.harvard.edu Sent: Tuesday, August 20, 2019 9:47 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Help with using family as random effect in sibling study
Sure! We have been conducting analyses in a large sample of pairs of siblings to see the effect of prenatal exposures on cortical thickness. For the current analysis, we're looking at the effect of the exposure load (total # of exposures) on cortical thickness using a paired-difference model, so the covariant being used is the difference in exposure load between each pair. We're trying to figure out if it is possible to also covary for the family the siblings belong to (using the assigned Family ID), to see the effect of family on cortical thickness as well as exposure load. This was able to be done statistically, however we weren't sure if it could be done in Freesurfer, too.
My apologies if this is still unclear - please let me know if you have any further questions. Thank you!
Best, Casey
--
Casey Hopkinson
Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Massachusetts General Hospital 149 13th Street, Charlestown, MA, 02129 (p) 617.643.3215
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Monday, August 19, 2019 6:29 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Help with using family as random effect in sibling study
I'm not sure I understand. Can you elaborate?
On 8/19/19 2:43 PM, Hopkinson, Casey E wrote:
Hello!
I am trying to generate significance maps for a paired-difference analysis of cortical thickness using multiple pairs of siblings, and was wondering if there is a way to incorporate the family ID as a random effect/covariate in Freesurfer. Is it possible for the family ID for each sibling pair to be used as a categorical/discrete variable to then see the effect of family on cortical thickness in addition to the main effects we are looking at? Any guidance would be greatly appreciated!
Best, Casey
*--*
*Casey Hopkinson*
Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Massachusetts General Hospital 149 13th Street, Charlestown, MA, 02129 (p) 617.643.3215
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
You could create a class for each family and assign each pair to a class. But this will not work unless you have multiple pairs per family for each family.
On 8/23/2019 9:01 AM, Hopkinson, Casey E wrote: Hi everyone,
Just wanted to follow up with this in case anyone may have an idea of if this can be done. Thanks!
--
Casey Hopkinson
Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Massachusetts General Hospital 149 13th Street, Charlestown, MA, 02129 (p) 617.643.3215
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Hopkinson, Casey E CHOPKINSON@mgh.harvard.edumailto:CHOPKINSON@mgh.harvard.edu Sent: Tuesday, August 20, 2019 9:47 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Help with using family as random effect in sibling study
Sure! We have been conducting analyses in a large sample of pairs of siblings to see the effect of prenatal exposures on cortical thickness. For the current analysis, we're looking at the effect of the exposure load (total # of exposures) on cortical thickness using a paired-difference model, so the covariant being used is the difference in exposure load between each pair. We're trying to figure out if it is possible to also covary for the family the siblings belong to (using the assigned Family ID), to see the effect of family on cortical thickness as well as exposure load. This was able to be done statistically, however we weren't sure if it could be done in Freesurfer, too.
My apologies if this is still unclear - please let me know if you have any further questions. Thank you!
Best, Casey
--
Casey Hopkinson
Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Massachusetts General Hospital 149 13th Street, Charlestown, MA, 02129 (p) 617.643.3215
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: Monday, August 19, 2019 6:29 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Help with using family as random effect in sibling study
I'm not sure I understand. Can you elaborate?
On 8/19/19 2:43 PM, Hopkinson, Casey E wrote:
Hello!
I am trying to generate significance maps for a paired-difference analysis of cortical thickness using multiple pairs of siblings, and was wondering if there is a way to incorporate the family ID as a random effect/covariate in Freesurfer. Is it possible for the family ID for each sibling pair to be used as a categorical/discrete variable to then see the effect of family on cortical thickness in addition to the main effects we are looking at? Any guidance would be greatly appreciated!
Best, Casey
*--*
*Casey Hopkinson*
Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Massachusetts General Hospital 149 13th Street, Charlestown, MA, 02129 (p) 617.643.3215
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug, thanks for getting back to me! So since we have just one pair of siblings per family, this way will not work?
--
Casey Hopkinson
Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Massachusetts General Hospital 149 13th Street, Charlestown, MA, 02129 (p) 617.643.3215
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Friday, August 23, 2019 10:17 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Help with using family as random effect in sibling study
You could create a class for each family and assign each pair to a class. But this will not work unless you have multiple pairs per family for each family.
On 8/23/2019 9:01 AM, Hopkinson, Casey E wrote: Hi everyone,
Just wanted to follow up with this in case anyone may have an idea of if this can be done. Thanks!
--
Casey Hopkinson
Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Massachusetts General Hospital 149 13th Street, Charlestown, MA, 02129 (p) 617.643.3215
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Hopkinson, Casey E CHOPKINSON@mgh.harvard.edumailto:CHOPKINSON@mgh.harvard.edu Sent: Tuesday, August 20, 2019 9:47 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Help with using family as random effect in sibling study
Sure! We have been conducting analyses in a large sample of pairs of siblings to see the effect of prenatal exposures on cortical thickness. For the current analysis, we're looking at the effect of the exposure load (total # of exposures) on cortical thickness using a paired-difference model, so the covariant being used is the difference in exposure load between each pair. We're trying to figure out if it is possible to also covary for the family the siblings belong to (using the assigned Family ID), to see the effect of family on cortical thickness as well as exposure load. This was able to be done statistically, however we weren't sure if it could be done in Freesurfer, too.
My apologies if this is still unclear - please let me know if you have any further questions. Thank you!
Best, Casey
--
Casey Hopkinson
Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Massachusetts General Hospital 149 13th Street, Charlestown, MA, 02129 (p) 617.643.3215
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: Monday, August 19, 2019 6:29 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Help with using family as random effect in sibling study
I'm not sure I understand. Can you elaborate?
On 8/19/19 2:43 PM, Hopkinson, Casey E wrote:
Hello!
I am trying to generate significance maps for a paired-difference analysis of cortical thickness using multiple pairs of siblings, and was wondering if there is a way to incorporate the family ID as a random effect/covariate in Freesurfer. Is it possible for the family ID for each sibling pair to be used as a categorical/discrete variable to then see the effect of family on cortical thickness in addition to the main effects we are looking at? Any guidance would be greatly appreciated!
Best, Casey
*--*
*Casey Hopkinson*
Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Massachusetts General Hospital 149 13th Street, Charlestown, MA, 02129 (p) 617.643.3215
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Greve, Douglas N.,Ph.D. -
Hopkinson, Casey E