qdec analysis with 2 covariates

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Jon Wieser

5 Dec 2013 5 Dec '13

2:57 p.m.

HI freesurfer experts

I want to do an analysis in qdec with 2 groups(ADHD, and Marijuana usage) and 2 covariates(age and gender) to study the effect of these factors on cortical thickness. I can only select a covariate in the qdec gui. is there a way to select both covariates in the qdec GUI? Thanks Jon

-- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219

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Douglas N Greve

9 Dec 9 Dec

2:48 p.m.

Hi Jon, QDEC does not currently allow more than one covariates of interest. You will have to use the command-line stream (ie, mris_preproc, mri_surf2surf, mri_glmfit, mri_glmfit-sim)

doug

On 12/05/2013 02:57 PM, Jon Wieser wrote:

...

HI freesurfer experts

I want to do an analysis in qdec with 2 groups(ADHD, and Marijuana usage) and 2 covariates(age and gender) to study the effect of these factors on cortical thickness. I can only select a covariate in the qdec gui. is there a way to select both covariates in the qdec GUI? Thanks Jon

Jon Wieser

3:01 p.m.

thanks doug,

We've run a 2x2 analysis for thickness in Qdec and want the get the average thickness value for each cluster, for each subject. How can i get a table of thickness data , for feach subject in the analysis Jon

----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Monday, December 9, 2013 1:48:15 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates

Hi Jon, QDEC does not currently allow more than one covariates of interest. You will have to use the command-line stream (ie, mris_preproc, mri_surf2surf, mri_glmfit, mri_glmfit-sim)

doug

On 12/05/2013 02:57 PM, Jon Wieser wrote:

...

HI freesurfer experts

I want to do an analysis in qdec with 2 groups(ADHD, and Marijuana usage) and 2 covariates(age and gender) to study the effect of these factors on cortical thickness. I can only select a covariate in the qdec gui. is there a way to select both covariates in the qdec GUI? Thanks Jon

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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 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.

Douglas N Greve

3:15 p.m.

It is in one of the output files. Look for the .dat file in mri_glmfit-sim --help

On 12/09/2013 03:01 PM, Jon Wieser wrote:

...

thanks doug,

We've run a 2x2 analysis for thickness in Qdec and want the get the average thickness value for each cluster, for each subject. How can i get a table of thickness data , for feach subject in the analysis Jon

----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Monday, December 9, 2013 1:48:15 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates

Hi Jon, QDEC does not currently allow more than one covariates of interest. You will have to use the command-line stream (ie, mris_preproc, mri_surf2surf, mri_glmfit, mri_glmfit-sim)

doug

On 12/05/2013 02:57 PM, Jon Wieser wrote:

...
HI freesurfer experts

I want to do an analysis in qdec with 2 groups(ADHD, and Marijuana usage) and 2 covariates(age and gender) to study the effect of these factors on cortical thickness. I can only select a covariate in the qdec gui. is there a way to select both covariates in the qdec GUI? Thanks Jon

Jon Wieser

5:09 p.m.

I found data for the average thickness all subjects for each cluster, but I haven't found the individual subject's thickness for each cluster. can you direct me to that data? Jon ----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Monday, December 9, 2013 2:15:39 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates

It is in one of the output files. Look for the .dat file in mri_glmfit-sim --help

On 12/09/2013 03:01 PM, Jon Wieser wrote:

...

thanks doug,

We've run a 2x2 analysis for thickness in Qdec and want the get the average thickness value for each cluster, for each subject. How can i get a table of thickness data , for feach subject in the analysis Jon

----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Monday, December 9, 2013 1:48:15 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates

Hi Jon, QDEC does not currently allow more than one covariates of interest. You will have to use the command-line stream (ie, mris_preproc, mri_surf2surf, mri_glmfit, mri_glmfit-sim)

doug

On 12/05/2013 02:57 PM, Jon Wieser wrote:

...
HI freesurfer experts

I want to do an analysis in qdec with 2 groups(ADHD, and Marijuana usage) and 2 covariates(age and gender) to study the effect of these factors on cortical thickness. I can only select a covariate in the qdec gui. is there a way to select both covariates in the qdec GUI? Thanks Jon

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 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.

Douglas N Greve

6:02 p.m.

which file did you look in? It should have a name like cache.th20.abs.y.ocn.dat

On 12/09/2013 05:09 PM, Jon Wieser wrote:

...

I found data for the average thickness all subjects for each cluster, but I haven't found the individual subject's thickness for each cluster. can you direct me to that data? Jon ----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Monday, December 9, 2013 2:15:39 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates

It is in one of the output files. Look for the .dat file in mri_glmfit-sim --help

On 12/09/2013 03:01 PM, Jon Wieser wrote:

...
thanks doug,

We've run a 2x2 analysis for thickness in Qdec and want the get the average thickness value for each cluster, for each subject. How can i get a table of thickness data , for feach subject in the analysis Jon

----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Monday, December 9, 2013 1:48:15 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates

Hi Jon, QDEC does not currently allow more than one covariates of interest. You will have to use the command-line stream (ie, mris_preproc, mri_surf2surf, mri_glmfit, mri_glmfit-sim)

doug

On 12/05/2013 02:57 PM, Jon Wieser wrote:

...
HI freesurfer experts

I want to do an analysis in qdec with 2 groups(ADHD, and Marijuana usage) and 2 covariates(age and gender) to study the effect of these factors on cortical thickness. I can only select a covariate in the qdec gui. is there a way to select both covariates in the qdec GUI? Thanks Jon

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Douglas N Greve
Jon Wieser