Re: [HCP-Users] Test-retest reliability / Intra vs inter subject variability of HCP data

2016-01-29 Thread Harms, Michael 




The ‘eddy’ correction may be better if it has both polarities to work with.  Splitting the polarities and processing them separately would be a “test/retest” that doesn’t necessarily reflect the HCP protocol.  The approx. 45 subjects that were repeated
 through the entire HCP protocol will allow one to assess the reliability of the full (intended) acquisition, albeit at a mean interval between visits of about 130 days.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From:  on behalf of Joelle Zimmermann 
Date: Friday, January 29, 2016 at 1:50 PM
To: "Harms, Michael" 
Cc: "hcp-users@humanconnectome.org" 
Subject: Re: [HCP-Users] Test-retest reliability / Intra vs inter subject variability of HCP data





Thank you all! Michael, why would you expect the two diffusion scans using the different phase encoding directions to be different? Or do you mean more as in that there is not enough time between 'test' and 'retest'?


Joelle


On Thu, Jan 28, 2016 at 10:13 PM, Harms, Michael 
 wrote:


There are about 45 subjects that went through the entire HCP protocol a
2nd time that will be a good way to assess the reliability of the
diffusion data when released later this spring.

Note that using one PE polarity as “test” and the other PE polarity as
“retest” would not really be testing the test/retest reliability of the
full diffusion protocol.

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 1/28/16, 8:04 PM, "hcp-users-boun...@humanconnectome.org on behalf of
David Van Essen"  wrote:

Data from several dozen test-retest subjects (I don’t recall the exact
number) is currently being processed and will be part of the S1200
release, currently targeted for mid-spring.

David VE

> On Jan 28, 2016, at 6:52 PM, Glasser, Matthew  wrote:
>
> There is some data that was collected for full rescans of the entire
> protocol, however I don¹t know the release plans for this data.
>
> Peace,
>
> Matt.
>
> On 1/28/16, 3:10 PM, "hcp-users-boun...@humanconnectome.org on behalf of
> dgw"  dgwake...@gmail.com> wrote:
>
>> Since most of HCP has each diffusion scan run twice (once each) with
>> different phase encode directions, you could analyze each of those
>> separately (only using the B0s from the opposite phase encode
>> direction). Then perform whatever test-retest tests you are interested
>> in. Note, that you will end up with slightly different masks using
>> this technique in eddy (I haven't been able to track down why). You
>> should try to come up with a way to control for this.
>>
>> hth
>> d
>>
>> On Thu, Jan 28, 2016 at 4:05 PM, Joelle Zimmermann
>>  wrote:
>>> Hi HCPers.
>>>
>>> I'm curious about the test-retest reliability and the inter subject
>>> versus
>>> intra subject variability of the HCP resting functional and diffusion
>>> data,
>>> particularly whether anyone has looked at this in SC and FC
>>>connectomes?
>>>
>>> To check this out in the rsFC data is simple, using the two scans (pre
>>> and
>>> post), or alternatively splitting the time series in half to look at
>>> reproducibility. But what about SC derived from diffusion data, since
>>> diffusion was measured only once the intra subject variability/ test
>>> retest.
>>> Does anyone know of a systematic check of variability in the SC data?
>>>
>>> Thanks,
>>> Joelle
>>>
>>> ___
>>> HCP-Users mailing list
>>> HCP-Users@humanconnectome.org
>>> 
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> 
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
>
> 
> The materials in this message are private and may contain Protected
>Healthcare Information or other information of a sensitive nature. If you
>are not the intended recipient, be advised that any unauthorized use,
>disclosure, copying or the taking of any action in reliance on the
>contents of this information

Re: [HCP-Users] Test-retest reliability / Intra vs inter subject variability of HCP data

2016-01-29 Thread Joelle Zimmermann 
Thank you all! Michael, why would you expect the two diffusion scans using
the different phase encoding directions to be different? Or do you mean
more as in that there is not enough time between 'test' and 'retest'?

Joelle

On Thu, Jan 28, 2016 at 10:13 PM, Harms, Michael  wrote:

>
> There are about 45 subjects that went through the entire HCP protocol a
> 2nd time that will be a good way to assess the reliability of the
> diffusion data when released later this spring.
>
> Note that using one PE polarity as “test” and the other PE polarity as
> “retest” would not really be testing the test/retest reliability of the
> full diffusion protocol.
>
> cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
>
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave.Tel: 314-747-6173
> St. Louis, MO  63110Email: mha...@wustl.edu
>
>
>
>
> On 1/28/16, 8:04 PM, "hcp-users-boun...@humanconnectome.org on behalf of
> David Van Essen"  vanes...@wustl.edu> wrote:
>
> Data from several dozen test-retest subjects (I don’t recall the exact
> number) is currently being processed and will be part of the S1200
> release, currently targeted for mid-spring.
>
> David VE
>
> > On Jan 28, 2016, at 6:52 PM, Glasser, Matthew 
> wrote:
> >
> > There is some data that was collected for full rescans of the entire
> > protocol, however I don¹t know the release plans for this data.
> >
> > Peace,
> >
> > Matt.
> >
> > On 1/28/16, 3:10 PM, "hcp-users-boun...@humanconnectome.org on behalf of
> > dgw"  > dgwake...@gmail.com> wrote:
> >
> >> Since most of HCP has each diffusion scan run twice (once each) with
> >> different phase encode directions, you could analyze each of those
> >> separately (only using the B0s from the opposite phase encode
> >> direction). Then perform whatever test-retest tests you are interested
> >> in. Note, that you will end up with slightly different masks using
> >> this technique in eddy (I haven't been able to track down why). You
> >> should try to come up with a way to control for this.
> >>
> >> hth
> >> d
> >>
> >> On Thu, Jan 28, 2016 at 4:05 PM, Joelle Zimmermann
> >>  wrote:
> >>> Hi HCPers.
> >>>
> >>> I'm curious about the test-retest reliability and the inter subject
> >>> versus
> >>> intra subject variability of the HCP resting functional and diffusion
> >>> data,
> >>> particularly whether anyone has looked at this in SC and FC
> >>>connectomes?
> >>>
> >>> To check this out in the rsFC data is simple, using the two scans (pre
> >>> and
> >>> post), or alternatively splitting the time series in half to look at
> >>> reproducibility. But what about SC derived from diffusion data, since
> >>> diffusion was measured only once the intra subject variability/ test
> >>> retest.
> >>> Does anyone know of a systematic check of variability in the SC data?
> >>>
> >>> Thanks,
> >>> Joelle
> >>>
> >>> ___
> >>> HCP-Users mailing list
> >>> HCP-Users@humanconnectome.org
> >>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> >> ___
> >> HCP-Users mailing list
> >> HCP-Users@humanconnectome.org
> >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> >
> >
> > 
> > The materials in this message are private and may contain Protected
> >Healthcare Information or other information of a sensitive nature. If you
> >are not the intended recipient, be advised that any unauthorized use,
> >disclosure, copying or the taking of any action in reliance on the
> >contents of this information is strictly prohibited. If you have received
> >this email in error, please immediately notify the sender via telephone
> >or return mail.
> >
> > ___
> > HCP-Users mailing list
> > HCP-Users@humanconnectome.org
> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
>
> 
> The materials in this message are private and may contain Protected
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> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
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>