Re: [Freesurfer] Regression: Activation as a function of condition

Hi Doug and Freesurfers,

Now that I have re-processed some of my data in Stable 5, I would like to re-open a previous problem I was trying to tackle:

" We are using the Sternberg Item Recognition Paradigm in our study, which involves the memorization and recognition of groups of 1, 3, 5, and 7 letters. Each run has two sets of each condition (load). We want to determine if any regions of the brain activate in a linear pattern with increased task load (# of letters). I have already done regression analyses using genotype, but that was between subjects, while this analysis would be within subjects. Does anyone know how I could structure an analysis that would allow me to look at this? Is this something I have to do at the mkanalysis-sess level?"

I had tried doing this in Stable 4 using the method described here https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-December/016557.... However, I was unable to generate the desired results, so I decided to switch over to Stable 5 as suggested.

Thanks,

Adam

---------------------------- Original Message ---------------------------- Subject: Re: [Freesurfer] Regression: Activation as a function of condition From: "Douglas N Greve" greve@nmr.mgh.harvard.edu Date: Tue, January 11, 2011 11:52 am To: "Adam Nitenson" nitenson@nmr.mgh.harvard.edu

---

You don't need to re-unpack. you don't run recon-all on the functional, only the anatomicals.

Adam Nitenson wrote:

...

So this means I will have to start at the unpacksdcmdir command and then recon-all to rerun the functionals?

...

You don't need to re-run the anatomicals, but you will need to rerun the functionals.

doug

Adam Nitenson wrote:

...

Hmm...it appears that we might need to make the transition over to Stable 5 then.

Would I have to reprocess all Stable 4 subjects again in Stable 5 (including the whole recon-all from bourget) process, or is there some sort of jumping off point from which I can start using the new stable?

Thanks,

Adam

...

you can't do it in stable4, but you can in stable 5.

doug

Adam Nitenson wrote:

...

Hello Freesurfers,

 We are using the Sternberg Item Recognition Paradigm in our

study, which involves the memorization and recognition of groups of 1, 3, 5, and 7 letters. Each run has two sets of each condition (load). We want to determine if any regions of the brain activate in a linear pattern with increased task load. I have already done regression analyses using genotype, but that was between subjects, while this analysis would be within subjects. Does anyone know how I could structure an analysis (STABLE 4) that would allow me to look at this? Is this something I have to do at the mkanalysis-sess level?

Thanks,

Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital