Re: [HCP-Users] Spatial smoothing of RS data

[David Hofmann]

Hi Matthew,

I must have somehow overlooked this information in the paper, thank you :).

greetings

David

2015-02-20 18:39 GMT+01:00 Glasser, Matthew :

>  A very minimal 2mm FWHM constrained to the grayordinates space (as a
> part of resampling to the grayordinates space).  See this paper:
>
>  http://www.sciencedirect.com/science/article/pii/S1053811913005053
>
>  I don’t recommend people apply any substantial spatial smoothing to HCP
> data because it destructively removes real (and interesting) individual
> differences.  Why bother using our high spatial and temporal resolution
> data if you’re just going to smooth it?
>
>  Peace,
>
>  Matt.
>
>   From: David Hofmann 
> Date: Friday, February 20, 2015 at 11:33 AM
> To: hcp-users 
> Subject: [HCP-Users] Spatial smoothing of RS data
>
>Hi,
>
>  I was wondering how much spatial smoothing was applied to the RS data
> (the data where the node timeseries are based upon) ?
>
>  greetings
>
>  David
>
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> Healthcare Information or other information of a sensitive nature. If you
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> of this information is strictly prohibited. If you have received this email
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Re: [HCP-Users] Spatial smoothing of RS data

[Glasser, Matthew]

A very minimal 2mm FWHM constrained to the grayordinates space (as a part of resampling to the grayordinates space).  See this paper:


http://www.sciencedirect.com/science/article/pii/S1053811913005053


I don’t recommend people apply any substantial spatial smoothing to HCP data because it destructively removes real (and interesting) individual differences.  Why bother using our high spatial and temporal resolution data if you’re just going to smooth
 it?


Peace,


Matt.




From: David Hofmann 
Date: Friday, February 20, 2015 at 11:33 AM
To: hcp-users 
Subject: [HCP-Users] Spatial smoothing of RS data








Hi,


I was wondering how much spatial smoothing was applied to the RS data (the data where the node timeseries are based upon) ?


greetings


David









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[HCP-Users] Spatial smoothing of RS data

[David Hofmann]

Hi,

I was wondering how much spatial smoothing was applied to the RS data (the
data where the node timeseries are based upon) ?

greetings

David

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Re: [HCP-Users] Myelin Mapping

[Barbara Kreilkamp]

Dear Matt,
Thank you for your quick reply.
Best wishes,
Barbara Anne

On Fri, Feb 20, 2015 at 1:49 PM, Glasser, Matthew 
wrote:

>  No it was a subsequent presentation on the same topic at a different
> meeting.
>
>  Peace,
>
>  Matt.
>
>   From: Seán Froudist Walsh 
> Date: Friday, February 20, 2015 at 7:48 AM
>
> To: Matt Glasser 
> Cc: Barbara Kreilkamp , "
> hcp-users@humanconnectome.org" 
> Subject: Re: [HCP-Users] Myelin Mapping
>
>   after the talk?
>
> On 20 February 2015 at 13:42, Glasser, Matthew 
> wrote:
>
>>  If I recall correctly, they withdrew their SFN 2014 presentation.  I
>> don’t know the reason for that.
>>
>>  Peace,
>>
>>  Matt.
>>
>>   From: Seán Froudist Walsh 
>> Date: Friday, February 20, 2015 at 7:27 AM
>> To: Matt Glasser 
>> Cc: Barbara Kreilkamp , "
>> hcp-users@humanconnectome.org" 
>> Subject: Re: [HCP-Users] Myelin Mapping
>>
>>   I wonder if you have an opinion on the talk by Stefano Sandrone from
>> Marco Catani's group at OHBM 2014 that showed that this measure doesn't
>> correlate with expected myelin patterns in white matter?
>>
>> On 20 February 2015 at 13:08, Glasser, Matthew 
>> wrote:
>>
>>>  Please use the HCP Minimal Preprocessing Pipelines to create T1w/T2w
>>> myelin maps with the latest code/methods (including bias correction and
>>> normalization):
>>>
>>>  https://github.com/Washington-University/Pipelines
>>>
>>>  You will need a T1w and a T2w images acquired in the same scanning
>>> session with the same image intensity filters (e.g. pre scan normalize or
>>> not) applied to both.  For myelin mapping only, a field map is optional
>>> (but recommended).
>>>
>>>  Peace,
>>>
>>>  Matt.
>>>
>>>   From: Barbara Kreilkamp 
>>> Date: Friday, February 20, 2015 at 7:04 AM
>>> To: "hcp-users@humanconnectome.org" 
>>> Subject: [HCP-Users] Myelin Mapping
>>>
>>>   Dear HCP- users,
>>>
>>> Could you please point me to a tutorial for myelin mapping with Human
>>> Connectome Workbench software?
>>> Also, is there a way to implement bias-correction for this technique?
>>> Thank you very much,
>>> Best wishes,
>>> Barbara
>>>
>>> ___
>>> 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
>>>
>>
>>
>>  --
>>
>> 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.
>>
>
>
>  --
>
> 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
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Re: [HCP-Users] Myelin Mapping

[Glasser, Matthew]

No it was a subsequent presentation on the same topic at a different meeting.


Peace,


Matt.




From: Seán Froudist Walsh 
Date: Friday, February 20, 2015 at 7:48 AM
To: Matt Glasser 
Cc: Barbara Kreilkamp , "hcp-users@humanconnectome.org" 
Subject: Re: [HCP-Users] Myelin Mapping





after the talk?

On 20 February 2015 at 13:42, Glasser, Matthew 
 wrote:


If I recall correctly, they withdrew their SFN 2014 presentation.  I don’t know the reason for that.  


Peace,


Matt.




From: Seán Froudist Walsh 
Date: Friday, February 20, 2015 at 7:27 AM
To: Matt Glasser 
Cc: Barbara Kreilkamp , "hcp-users@humanconnectome.org" 
Subject: Re: [HCP-Users] Myelin Mapping







I wonder if you have an opinion on the talk by Stefano Sandrone from Marco Catani's group at OHBM 2014 that showed that this measure doesn't correlate with expected myelin patterns in white matter? 

On 20 February 2015 at 13:08, Glasser, Matthew 
 wrote:


Please use the HCP Minimal Preprocessing Pipelines to create T1w/T2w myelin maps with the latest code/methods (including bias correction and normalization):


https://github.com/Washington-University/Pipelines


You will need a T1w and a T2w images acquired in the same scanning session with the same image intensity filters (e.g. pre scan normalize or not) applied to both.  For myelin mapping only, a field map is optional (but recommended).  


Peace,


Matt.




From: Barbara Kreilkamp 
Date: Friday, February 20, 2015 at 7:04 AM
To: "hcp-users@humanconnectome.org" 
Subject: [HCP-Users] Myelin Mapping







Dear HCP- users,

Could you please point me to a tutorial for myelin mapping with Human Connectome Workbench software?
Also, is there a way to implement bias-correction for this technique?
Thank you very much,
Best wishes,
Barbara

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 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.

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 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
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Re: [HCP-Users] Myelin Mapping

[Seán Froudist Walsh]

after the talk?

On 20 February 2015 at 13:42, Glasser, Matthew 
wrote:

>  If I recall correctly, they withdrew their SFN 2014 presentation.  I
> don’t know the reason for that.
>
>  Peace,
>
>  Matt.
>
>   From: Seán Froudist Walsh 
> Date: Friday, February 20, 2015 at 7:27 AM
> To: Matt Glasser 
> Cc: Barbara Kreilkamp , "
> hcp-users@humanconnectome.org" 
> Subject: Re: [HCP-Users] Myelin Mapping
>
>   I wonder if you have an opinion on the talk by Stefano Sandrone from
> Marco Catani's group at OHBM 2014 that showed that this measure doesn't
> correlate with expected myelin patterns in white matter?
>
> On 20 February 2015 at 13:08, Glasser, Matthew 
> wrote:
>
>>  Please use the HCP Minimal Preprocessing Pipelines to create T1w/T2w
>> myelin maps with the latest code/methods (including bias correction and
>> normalization):
>>
>>  https://github.com/Washington-University/Pipelines
>>
>>  You will need a T1w and a T2w images acquired in the same scanning
>> session with the same image intensity filters (e.g. pre scan normalize or
>> not) applied to both.  For myelin mapping only, a field map is optional
>> (but recommended).
>>
>>  Peace,
>>
>>  Matt.
>>
>>   From: Barbara Kreilkamp 
>> Date: Friday, February 20, 2015 at 7:04 AM
>> To: "hcp-users@humanconnectome.org" 
>> Subject: [HCP-Users] Myelin Mapping
>>
>>   Dear HCP- users,
>>
>> Could you please point me to a tutorial for myelin mapping with Human
>> Connectome Workbench software?
>> Also, is there a way to implement bias-correction for this technique?
>> Thank you very much,
>> Best wishes,
>> Barbara
>>
>> ___
>> 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
>>
>
>
>  --
>
> 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.
>

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Re: [HCP-Users] Myelin Mapping

[Glasser, Matthew]

If I recall correctly, they withdrew their SFN 2014 presentation.  I don’t know the reason for that.  


Peace,


Matt.




From: Seán Froudist Walsh 
Date: Friday, February 20, 2015 at 7:27 AM
To: Matt Glasser 
Cc: Barbara Kreilkamp , "hcp-users@humanconnectome.org" 
Subject: Re: [HCP-Users] Myelin Mapping





I wonder if you have an opinion on the talk by Stefano Sandrone from Marco Catani's group at OHBM 2014 that showed that this measure doesn't correlate with expected myelin patterns in white matter? 

On 20 February 2015 at 13:08, Glasser, Matthew 
 wrote:


Please use the HCP Minimal Preprocessing Pipelines to create T1w/T2w myelin maps with the latest code/methods (including bias correction and normalization):


https://github.com/Washington-University/Pipelines


You will need a T1w and a T2w images acquired in the same scanning session with the same image intensity filters (e.g. pre scan normalize or not) applied to both.  For myelin mapping only, a field map is optional (but recommended).  


Peace,


Matt.




From: Barbara Kreilkamp 
Date: Friday, February 20, 2015 at 7:04 AM
To: "hcp-users@humanconnectome.org" 
Subject: [HCP-Users] Myelin Mapping







Dear HCP- users,

Could you please point me to a tutorial for myelin mapping with Human Connectome Workbench software?
Also, is there a way to implement bias-correction for this technique?
Thank you very much,
Best wishes,
Barbara

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 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.

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Re: [HCP-Users] Myelin Mapping

[Seán Froudist Walsh]

I wonder if you have an opinion on the talk by Stefano Sandrone from Marco
Catani's group at OHBM 2014 that showed that this measure doesn't correlate
with expected myelin patterns in white matter?

On 20 February 2015 at 13:08, Glasser, Matthew 
wrote:

>  Please use the HCP Minimal Preprocessing Pipelines to create T1w/T2w
> myelin maps with the latest code/methods (including bias correction and
> normalization):
>
>  https://github.com/Washington-University/Pipelines
>
>  You will need a T1w and a T2w images acquired in the same scanning
> session with the same image intensity filters (e.g. pre scan normalize or
> not) applied to both.  For myelin mapping only, a field map is optional
> (but recommended).
>
>  Peace,
>
>  Matt.
>
>   From: Barbara Kreilkamp 
> Date: Friday, February 20, 2015 at 7:04 AM
> To: "hcp-users@humanconnectome.org" 
> Subject: [HCP-Users] Myelin Mapping
>
>   Dear HCP- users,
>
> Could you please point me to a tutorial for myelin mapping with Human
> Connectome Workbench software?
> Also, is there a way to implement bias-correction for this technique?
> Thank you very much,
> Best wishes,
> Barbara
>
> ___
> 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
>

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Re: [HCP-Users] Myelin Mapping

[Glasser, Matthew]

Please use the HCP Minimal Preprocessing Pipelines to create T1w/T2w myelin maps with the latest code/methods (including bias correction and normalization):


https://github.com/Washington-University/Pipelines


You will need a T1w and a T2w images acquired in the same scanning session with the same image intensity filters (e.g. pre scan normalize or not) applied to both.  For myelin mapping only, a field map is optional (but recommended).  


Peace,


Matt.




From: Barbara Kreilkamp 
Date: Friday, February 20, 2015 at 7:04 AM
To: "hcp-users@humanconnectome.org" 
Subject: [HCP-Users] Myelin Mapping





Dear HCP- users,

Could you please point me to a tutorial for myelin mapping with Human Connectome Workbench software?
Also, is there a way to implement bias-correction for this technique?
Thank you very much,
Best wishes,
Barbara

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[HCP-Users] Myelin Mapping

[Barbara Kreilkamp]

Dear HCP- users,

Could you please point me to a tutorial for myelin mapping with Human
Connectome Workbench software?
Also, is there a way to implement bias-correction for this technique?
Thank you very much,
Best wishes,
Barbara

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[HCP-Users] Myelin Mapping

[Barbara Kreilkamp]

Dear HCP- users,

Could you please point me to a tutorial for myelin mapping with Human
Connectome Workbench software?
Also, is there a way to implement bias-correction for this technique?
Thank you very much,
Best wishes,
Barbara

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