The Something-vs-fix of the original paradigm will not relate to the 2-v-fix of the slope test, though they should look something like the 1-v-fix of the slope test. Have you looked at that? The 2-v-fix will look more like a difference in the loads from the original (eg, 7-1).

doug

Adam Nitenson wrote:

The supposed "load regression map" that I generated did not make sense given the maps of the individual loads vs fix. I attached the original paradigm (run1.par), the slope paradigm which I tried to adapt from the other thread (SIRP_Run1_LoadSlopeTest.par) and an image showing the 1vfix, 3vfix, 5vfix, and 7vfix images from the original paradigm, as well as a large 2vFix image from the new paradigm, which I thought would have shown the within subjects regression (condition 2 being the weighted loads). "Desired results" was a poor description...it is more that the results do not seems to represent the load regression based on the individual load maps.

-Adam

...

what do you mean that you were not able to get the desired result? doug

Adam Nitenson wrote:

...

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 _______________________________________________ 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

The 1vFix for the altered paradigm looks like the something vs fix for the original, so that is good. To my eye, the 2vFix for the altered looks reasonable, but you're right that it's hard to tell. A better comparison is to compare 2vFix for the altered against something like 7v3 or 5v1. There is nothing new in version 5 in this regard.

doug

Adam Nitenson wrote:

Sorry for the delayed reply...I actually had to tweak the weighted paradigm for the slope a bit since selxavg3 kept failing. The reason was that the analysis called for conditions 0-9 and not all of them were included in that weighted paradigm file...(not quite sure why it worked the first time, however).

Anyway, I've attached images from one subject, similar to my last email, with the original SIRP analysis on top and the 1vfix and 2vfix from the edited weighted paradigm below (and I've attached an example of that edited paradigm, "paradigm" and the original SIRP paradigm "run1.par"). It's still hard to tell, for myself, if the new 1vFix is indeed representative of the areas displaying activation with a significant linear relationship to task load size. Is this weighted paradigm method the best way to do this type of analysis, or does Stable 5 introduce any alternate methods?

Thanks,

Adam

...

The Something-vs-fix of the original paradigm will not relate to the 2-v-fix of the slope test, though they should look something like the 1-v-fix of the slope test. Have you looked at that? The 2-v-fix will look more like a difference in the loads from the original (eg, 7-1).

doug

Adam Nitenson wrote:

...

The supposed "load regression map" that I generated did not make sense given the maps of the individual loads vs fix. I attached the original paradigm (run1.par), the slope paradigm which I tried to adapt from the other thread (SIRP_Run1_LoadSlopeTest.par) and an image showing the 1vfix, 3vfix, 5vfix, and 7vfix images from the original paradigm, as well as a large 2vFix image from the new paradigm, which I thought would have shown the within subjects regression (condition 2 being the weighted loads). "Desired results" was a poor description...it is more that the results do not seems to represent the load regression based on the individual load maps.

-Adam

...

what do you mean that you were not able to get the desired result? doug

Adam Nitenson wrote:

...

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 _______________________________________________ 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 nitenson@nmr.mgh.harvard.edu Phone: 617-643-3215

---

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer