External Email - Use Caution
Hello,
I am trying to perform a paired analysis for a data set that has subjects' who belong to either group1 or group2 and have data at time point1 (tp1) and time point2 (tp2). I am following all the steps on the wiki but I want to clarify if the contrasts I plan to use for my analyses are appropriate.
For my analyses, I only have two groups and no covariates. I am interested to know if the decrease in cortical thickness of subjects in group 1 across tp1 and tp2 is more than the decrease in cortical thickness of subjects in group 2 across tp1 and tp2. The contrast I think should be used for this is: 1 -1. Is that correct?
I am also interested to know if the cortical thickness decreased for subjects regardless of the groups so should I use the contrast: 1 for that?
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
On 10/24/2018 09:45 PM, srishti goel wrote:
External Email - Use Caution
Hello,
I am trying to perform a paired analysis for a data set that has subjects' who belong to either group1 or group2 and have data at time point1 (tp1) and time point2 (tp2). I am following all the steps on the wiki but I want to clarify if the contrasts I plan to use for my analyses are appropriate.
For my analyses, I only have two groups and no covariates. I am interested to know if the decrease in cortical thickness of subjects in group 1 across tp1 and tp2 is more than the decrease in cortical thickness of subjects in group 2 across tp1 and tp2. The contrast I think should be used for this is: 1 -1. Is that correct?
Yes, if you first take the difference between tp1 and tp2.
I am also interested to know if the cortical thickness decreased for subjects regardless of the groups so should I use the contrast: 1 for that?
Assuming you are keeping 2 groups, then use 0.5 0.5
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu mailto:srishtig@email.unc.edu skype: srishti.goel12
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Douglas,
Thank you so much for your response. We just want to be extra careful about the way we are doing this and so below I have outlined the exact pattern of the group descriptor files we are using along with the contrast. Please let me know if you think this is correct or not. The questions we are asking with this analysis are the same as I outlined in the previous email.
*This is our first group descriptor file:*
GroupDescriptorFile 1 Title BEIP 8 vs. 16 compare CAU (0) And FCG (1) Class Main Input 005_16.long.005 Main Input 005_8.long.005 Main Input 006_16.long.006 Main Input 006_8.long.006 Main
*This is our second group descriptor file:*
GroupDescriptorFile 1 Title BEIP longitudinal Compare CAU (0) And FCG (1) Class cau Class fc Input 005_long_pair fc Input 006_long_pair cau
The contrast to understand group differences in thickness between 8 and 16 yr old data sets are: 1 -1
*Question1:* Is this correct? *Question 2:* If we use the below mentioned way to set up our second group descriptor file, will the above contrasts still work? Or can we use 0 1 contrast with the file below to get at the same thing? We actually ran it both ways and the results weren't similar but I specifically ask this question because we are a little worried about the above 'second group descriptor file' not having a column that says 'Main' and we are trying to understand the right way to do our analyses.
*Example group descriptor file 2:* GroupDescriptorFile 1 Title BEIP longitudinal Compare CAU (0) And FCG (1) Class Main Variables group Input 005_long_pair Main 1 Input 006_long_pair Main 0
Thank you so much! I appreciate all your help with this!
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
On Wed, Nov 7, 2018 at 9:24 AM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
On 10/24/2018 09:45 PM, srishti goel wrote:
External Email - Use CautionHello,
I am trying to perform a paired analysis for a data set that has subjects' who belong to either group1 or group2 and have data at time point1 (tp1) and time point2 (tp2). I am following all the steps on the wiki but I want to clarify if the contrasts I plan to use for my analyses are appropriate.
For my analyses, I only have two groups and no covariates. I am interested to know if the decrease in cortical thickness of subjects in group 1 across tp1 and tp2 is more than the decrease in cortical thickness of subjects in group 2 across tp1 and tp2. The contrast I think should be used for this is: 1 -1. Is that correct?
Yes, if you first take the difference between tp1 and tp2.
I am also interested to know if the cortical thickness decreased for subjects regardless of the groups so should I use the contrast: 1 for that?
Assuming you are keeping 2 groups, then use 0.5 0.5
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu mailto:srishtig@email.unc.edu skype: srishti.goel12
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
External Email - Use Caution
Hi Douglas,
Thank you so much for your response. We just want to be extra careful about the way we are doing this and so below I have outlined the exact pattern of the group descriptor files we are using along with the contrast. Please let me know if you think this is correct or not. The questions we are asking with this analysis are the same as I outlined in the previous email.
*This is our first group descriptor file:*
GroupDescriptorFile 1 Title BEIP 8 vs. 16 compare CAU (0) And FCG (1) Class Main Input 005_16.long.005 Main Input 005_8.long.005 Main Input 006_16.long.006 Main Input 006_8.long.006 Main
*This is our second group descriptor file:*
GroupDescriptorFile 1 Title BEIP longitudinal Compare CAU (0) And FCG (1) Class cau Class fc Input 005_long_pair fc Input 006_long_pair cau
The contrast to understand group differences in thickness between 8 and 16 yr old data sets are: 1 -1
*Question1:* Is this correct? *Question 2:* If we use the below mentioned way to set up our second group descriptor file, will the above contrasts still work? Or can we use 0 1 contrast with the file below to get at the same thing? We actually ran it both ways and the results weren't similar but I specifically ask this question because we are a little worried about the above 'second group descriptor file' not having a column that says 'Main' and we are trying to understand the right way to do our analyses.
*Example group descriptor file 2:* GroupDescriptorFile 1 Title BEIP longitudinal Compare CAU (0) And FCG (1) Class Main Variables group Input 005_long_pair Main 1 Input 006_long_pair Main 0
Thank you so much! I appreciate all your help with this!
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
On Wed, Nov 14, 2018 at 2:50 PM srishti goel 23srishtigoel@gmail.com wrote:
Hi Douglas,
Thank you so much for your response. We just want to be extra careful about the way we are doing this and so below I have outlined the exact pattern of the group descriptor files we are using along with the contrast. Please let me know if you think this is correct or not. The questions we are asking with this analysis are the same as I outlined in the previous email.
*This is our first group descriptor file:*
GroupDescriptorFile 1 Title BEIP 8 vs. 16 compare CAU (0) And FCG (1) Class Main Input 005_16.long.005 Main Input 005_8.long.005 Main Input 006_16.long.006 Main Input 006_8.long.006 Main
*This is our second group descriptor file:*
GroupDescriptorFile 1 Title BEIP longitudinal Compare CAU (0) And FCG (1) Class cau Class fc Input 005_long_pair fc Input 006_long_pair cau
The contrast to understand group differences in thickness between 8 and 16 yr old data sets are: 1 -1
*Question1:* Is this correct? *Question 2:* If we use the below mentioned way to set up our second group descriptor file, will the above contrasts still work? Or can we use 0 1 contrast with the file below to get at the same thing? We actually ran it both ways and the results weren't similar but I specifically ask this question because we are a little worried about the above 'second group descriptor file' not having a column that says 'Main' and we are trying to understand the right way to do our analyses.
*Example group descriptor file 2:* GroupDescriptorFile 1 Title BEIP longitudinal Compare CAU (0) And FCG (1) Class Main Variables group Input 005_long_pair Main 1 Input 006_long_pair Main 0
Thank you so much! I appreciate all your help with this!
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
On Wed, Nov 7, 2018 at 9:24 AM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
On 10/24/2018 09:45 PM, srishti goel wrote:
External Email - Use CautionHello,
I am trying to perform a paired analysis for a data set that has subjects' who belong to either group1 or group2 and have data at time point1 (tp1) and time point2 (tp2). I am following all the steps on the wiki but I want to clarify if the contrasts I plan to use for my analyses are appropriate.
For my analyses, I only have two groups and no covariates. I am interested to know if the decrease in cortical thickness of subjects in group 1 across tp1 and tp2 is more than the decrease in cortical thickness of subjects in group 2 across tp1 and tp2. The contrast I think should be used for this is: 1 -1. Is that correct?
Yes, if you first take the difference between tp1 and tp2.
I am also interested to know if the cortical thickness decreased for subjects regardless of the groups so should I use the contrast: 1 for that?
Assuming you are keeping 2 groups, then use 0.5 0.5
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu mailto:srishtig@email.unc.edu skype: srishti.goel12
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
answers below
On 11/21/2018 01:53 PM, srishti goel wrote:
External Email - Use Caution
Hi Douglas,
Thank you so much for your response. We just want to be extra careful about the way we are doing this and so below I have outlined the exact pattern of the group descriptor files we are using along with the contrast. Please let me know if you think this is correct or not. The questions we are asking with this analysis are the same as I outlined in the previous email.
_This is our first group descriptor file:_
GroupDescriptorFile 1 Title BEIP 8 vs. 16 compare CAU (0) And FCG (1) Class Main Input 005_16.long.005 Main Input 005_8.long.005 Main Input 006_16.long.006 Main Input 006_8.long.006 Main
_This is our second group descriptor file:_
GroupDescriptorFile 1 Title BEIP longitudinal Compare CAU (0) And FCG (1) Class cau Class fc Input 005_long_pair fc Input 006_long_pair cau
The contrast to understand group differences in thickness between 8 and 16 yr old data sets are: 1 -1
*Question1:* Is this correct?
Yes
*Question 2:* If we use the below mentioned way to set up our second group descriptor file, will the above contrasts still work? Or can we use 0 1 contrast with the file below to get at the same thing? We actually ran it both ways and the results weren't similar but I specifically ask this question because we are a little worried about the above 'second group descriptor file' not having a column that says 'Main' and we are trying to understand the right way to do our analyses.
I think this will give you the same answer.
_Example group descriptor file 2:_ GroupDescriptorFile 1 Title BEIP longitudinal Compare CAU (0) And FCG (1) Class Main Variables group Input 005_long_pair Main 1 Input 006_long_pair Main 0
Thank you so much! I appreciate all your help with this!
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu mailto:srishtig@email.unc.edu skype: srishti.goel12
On Wed, Nov 14, 2018 at 2:50 PM srishti goel <23srishtigoel@gmail.com mailto:23srishtigoel@gmail.com> wrote:
Hi Douglas, Thank you so much for your response. We just want to be extra careful about the way we are doing this and so below I have outlined the exact pattern of the group descriptor files we are using along with the contrast. Please let me know if you think this is correct or not. The questions we are asking with this analysis are the same as I outlined in the previous email. _This is our first group descriptor file:_ GroupDescriptorFile 1 Title BEIP 8 vs. 16 compare CAU (0) And FCG (1) Class Main Input 005_16.long.005 Main Input 005_8.long.005 Main Input 006_16.long.006 Main Input 006_8.long.006 Main _This is our second group descriptor file:_ GroupDescriptorFile 1 Title BEIP longitudinal Compare CAU (0) And FCG (1) Class cau Class fc Input 005_long_pair fc Input 006_long_pair cau The contrast to understand group differences in thickness between 8 and 16 yr old data sets are: 1 -1 *Question1:* Is this correct? *Question 2:* If we use the below mentioned way to set up our second group descriptor file, will the above contrasts still work? Or can we use 0 1 contrast with the file below to get at the same thing? We actually ran it both ways and the results weren't similar but I specifically ask this question because we are a little worried about the above 'second group descriptor file' not having a column that says 'Main' and we are trying to understand the right way to do our analyses. _Example group descriptor file 2:_ GroupDescriptorFile 1 Title BEIP longitudinal Compare CAU (0) And FCG (1) Class Main Variables group Input 005_long_pair Main 1 Input 006_long_pair Main 0 Thank you so much! I appreciate all your help with this! Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu <mailto:srishtig@email.unc.edu> skype: srishti.goel12 On Wed, Nov 7, 2018 at 9:24 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote: On 10/24/2018 09:45 PM, srishti goel wrote: > > External Email - Use Caution > > Hello, > > I am trying to perform a paired analysis for a data set that has > subjects' who belong to either group1 or group2 and have data at time > point1 (tp1) and time point2 (tp2). I am following all the steps on > the wiki but I want to clarify if the contrasts I plan to use for my > analyses are appropriate. > > For my analyses, I only have two groups and no covariates. I am > interested to know if the decrease in cortical thickness of subjects > in group 1 across tp1 and tp2 is more than the decrease in cortical > thickness of subjects in group 2 across tp1 and tp2. The contrast I > think should be used for this is: 1 -1. Is that correct? Yes, if you first take the difference between tp1 and tp2. > > I am also interested to know if the cortical thickness decreased for > subjects regardless of the groups so should I use the contrast: 1 for > that? Assuming you are keeping 2 groups, then use 0.5 0.5 > > Best, > Srishti > Social/Clinical Research Specialist > Child Imaging Research and Life Experiences Lab > University of North Carolina at Chapel Hill > email (W): srishtig@email.unc.edu <mailto:srishtig@email.unc.edu> <mailto:srishtig@email.unc.edu <mailto:srishtig@email.unc.edu>> > skype: srishti.goel12 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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srishti goel