Re: [HCP-Users] phase encoding and group ICA

2015-11-25 Thread Harms, Michael 







As a brief follow-up to this:  As you see from Steve's pasted code, the order of the time series in the PTN is based solely on the file name in ConnectomeDB.  Importantly, nothing in the REST{1,2}_{LR,RL} naming tells you whether the LR run came first,
 or vice-versa.  All you know for sure is that REST1 runs came before REST2.  (Most typically, a day beforehand, but a minority of subjects have multiple days between their REST1 and REST2 sessions).  While there is a prototypical temporal ordering of the runs,
 which would hold for the vast majority of subjects, on infrequent occasions that ordering might have been violated -- e.g., if a scan had to be reacquired.  


So, if you are investigating something that explicitly and critically depends on knowing the exact order in which the LR/RL runs were acquired for each and every subject, then you will have to pull the series acquisition times from the database.  There
 is a previous post to the list with details on how to do that.  Off the top of my head, I can't remember if that post included a mechanism to also get the number of days between the REST1 and REST2 sessions.  We've talked about making those sort of details
 more readily available, but it hasn't been a priority.


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: Stephen Smith <st...@fmrib.ox.ac.uk>
Date: Wednesday, November 25, 2015 1:18 AM
To: Mary Beth <m...@jhmi.edu>
Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] phase encoding and group ICA





Hi - 


Wrt group-ICA, it makes no difference what order the data was fed into the MIGP group-PCA.


Wrt the 4 chunks combined into the node timeseries in the 500-subject PTN release:  the order is always the following, so you will need to take into account the information you pasted below if you want to know about how this interacts with session
 orderings.



ff{1}=sprintf('%s/%d/RESOURCES/rfMRI_REST1_LR_FIX/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii',SUBJECTS,subID);
ff{2}=sprintf('%s/%d/RESOURCES/rfMRI_REST1_RL_FIX/rfMRI_REST1_RL/rfMRI_REST1_RL_Atlas_hp2000_clean.dtseries.nii',SUBJECTS,subID);
ff{3}=sprintf('%s/%d/RESOURCES/rfMRI_REST2_LR_FIX/rfMRI_REST2_LR/rfMRI_REST2_LR_Atlas_hp2000_clean.dtseries.nii',SUBJECTS,subID);
ff{4}=sprintf('%s/%d/RESOURCES/rfMRI_REST2_RL_FIX/rfMRI_REST2_RL/rfMRI_REST2_RL_Atlas_hp2000_clean.dtseries.nii',SUBJECTS,subID);



Cheers, Steve.


ps - for the 900 PTN release we will be releasing the code used to generate it.









On 25 Nov 2015, at 01:17, Mary Beth <m...@jhmi.edu> wrote:


The subject-specific parcel timeseries were provided in a single text file for each model order with 4800 time points each. I am trying to figure out if time points 2401-3600 from those text files always correspond to the LR session from
 Day 2, or if they correspond to the RL session from Day 2 for the handful of subjects collected before  1 October 2012 and the LR session from Day 2 for everyone else. I just want to make sure that I label everything correctly.
I hope this clarifies my question. Thanks again for your help.
-mb


On Tue, Nov 24, 2015, 19:29 Glasser, Matthew <glass...@wustl.edu> wrote:



I’m still not following why it matters.


Peace,


Matt.




From: Mary Beth <m...@jhmi.edu>
Date: Tuesday, November 24, 2015 at 6:18 PM
To: Matt Glasser <glass...@wustl.edu>, "hcp-users@humanconnectome.org"
 <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] phase encoding and group ICA








I just want to make sure I'm comparing apples to apples when I use the subject-specific timeseries. 


best,
mb



On Tue, Nov 24, 2015 at 7:11 PM Glasser, Matthew <glass...@wustl.edu> wrote:



Why does the order of the individual subject sessions matter for group ICA or PTNs?


Peace,


Matt.




From: <hcp-users-boun...@humanconnectome.org> on behalf of Mary Beth <m...@jhmi.edu>
Date: Tuesday, November 24, 2015 at 5:59 PM
To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
Subject: [HCP-Users] phase encoding and group ICA












Hi all,

According to this page 
http://www.humanconnectome.org/documentation/Q1/data-in-this-release.html, prior to 1 October 2012, the first resting state session of each visit was acquired with RL phase encoding, and the second session was acquired with LR phase encoding (RL/LR).  After
 this date, the first visit continued to be acquired in the RL/LR order, but the second visit was acquired in the opposite order, with the LR acquisition followed by the RL acquisition (LR/RL).


Here's my question: prior to group ICA and the generation

Re: [HCP-Users] phase encoding and group ICA

2015-11-24 Thread Glasser, Matthew 
Why does the order of the individual subject sessions matter for group ICA or 
PTNs?

Peace,

Matt.

From: 
>
 on behalf of Mary Beth >
Date: Tuesday, November 24, 2015 at 5:59 PM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] phase encoding and group ICA

Hi all,

According to this page 
http://www.humanconnectome.org/documentation/Q1/data-in-this-release.html, 
prior to 1 October 2012, the first resting state session of each visit was 
acquired with RL phase encoding, and the second session was acquired with LR 
phase encoding (RL/LR).  After this date, the first visit continued to be 
acquired in the RL/LR order, but the second visit was acquired in the opposite 
order, with the LR acquisition followed by the RL acquisition (LR/RL).

Here's my question: prior to group ICA and the generation of subject-specific 
sets of node timeseries in the August, 2014 "HCP500-PTN" 
(Parcellation+Timeseries+Netmats) data release, were the sessions for subjects 
acquired before 1 October 2012 reordered to match the order of sessions for 
subjects acquired after 1 October 2012?

Thanks in advance,
Mary Beth

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Re: [HCP-Users] phase encoding and group ICA

2015-11-24 Thread Mary Beth 
The subject-specific parcel timeseries were provided in a single text file
for each model order with 4800 time points each. I am trying to figure out
if time points 2401-3600 from those text files always correspond to the LR
session from Day 2, or if they correspond to the RL session from Day 2 for
the handful of subjects collected before  1 October 2012 and the LR session
from Day 2 for everyone else. I just want to make sure that I label
everything correctly.

I hope this clarifies my question. Thanks again for your help.

-mb

On Tue, Nov 24, 2015, 19:29 Glasser, Matthew <glass...@wustl.edu> wrote:

> I’m still not following why it matters.
>
> Peace,
>
> Matt.
>
> From: Mary Beth <m...@jhmi.edu>
> Date: Tuesday, November 24, 2015 at 6:18 PM
> To: Matt Glasser <glass...@wustl.edu>, "hcp-users@humanconnectome.org" <
> hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] phase encoding and group ICA
>
> I just want to make sure I'm comparing apples to apples when I use the
> subject-specific timeseries.
>
> best,
> mb
>
> On Tue, Nov 24, 2015 at 7:11 PM Glasser, Matthew <glass...@wustl.edu>
> wrote:
>
>> Why does the order of the individual subject sessions matter for group
>> ICA or PTNs?
>>
>> Peace,
>>
>> Matt.
>>
>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Mary Beth <
>> m...@jhmi.edu>
>> Date: Tuesday, November 24, 2015 at 5:59 PM
>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> Subject: [HCP-Users] phase encoding and group ICA
>>
>> Hi all,
>>
>> According to this page
>> http://www.humanconnectome.org/documentation/Q1/data-in-this-release.html,
>> prior to 1 October 2012, the first resting state session of each visit was
>> acquired with RL phase encoding, and the second session was acquired with
>> LR phase encoding (RL/LR).  After this date, the first visit continued to
>> be acquired in the RL/LR order, but the second visit was acquired in the
>> opposite order, with the LR acquisition followed by the RL acquisition
>> (LR/RL).
>>
>> Here's my question: prior to group ICA and the generation of
>> subject-specific sets of node timeseries in the August, 2014 “HCP500-PTN”
>> (Parcellation+Timeseries+Netmats) data release, were the sessions for
>> subjects acquired before 1 October 2012 reordered to match the order of
>> sessions for subjects acquired after 1 October 2012?
>>
>> Thanks in advance,
>> Mary Beth
>>
>> ___
>> 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
> in error, please immediately notify the sender via telephone or return mail.
>

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Re: [HCP-Users] phase encoding and group ICA

2015-11-24 Thread Stephen Smith 
Hi - 

Wrt group-ICA, it makes no difference what order the data was fed into the MIGP 
group-PCA.

Wrt the 4 chunks combined into the node timeseries in the 500-subject PTN 
release:  the order is always the following, so you will need to take into 
account the information you pasted below if you want to know about how this 
interacts with session orderings.

ff{1}=sprintf('%s/%d/RESOURCES/rfMRI_REST1_LR_FIX/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii',SUBJECTS,subID);
ff{2}=sprintf('%s/%d/RESOURCES/rfMRI_REST1_RL_FIX/rfMRI_REST1_RL/rfMRI_REST1_RL_Atlas_hp2000_clean.dtseries.nii',SUBJECTS,subID);
ff{3}=sprintf('%s/%d/RESOURCES/rfMRI_REST2_LR_FIX/rfMRI_REST2_LR/rfMRI_REST2_LR_Atlas_hp2000_clean.dtseries.nii',SUBJECTS,subID);
ff{4}=sprintf('%s/%d/RESOURCES/rfMRI_REST2_RL_FIX/rfMRI_REST2_RL/rfMRI_REST2_RL_Atlas_hp2000_clean.dtseries.nii',SUBJECTS,subID);

Cheers, Steve.

ps - for the 900 PTN release we will be releasing the code used to generate it.




> On 25 Nov 2015, at 01:17, Mary Beth <m...@jhmi.edu> wrote:
> 
> The subject-specific parcel timeseries were provided in a single text file 
> for each model order with 4800 time points each. I am trying to figure out if 
> time points 2401-3600 from those text files always correspond to the LR 
> session from Day 2, or if they correspond to the RL session from Day 2 for 
> the handful of subjects collected before  1 October 2012 and the LR session 
> from Day 2 for everyone else. I just want to make sure that I label 
> everything correctly.
> 
> I hope this clarifies my question. Thanks again for your help.
> 
> -mb
> 
> 
> On Tue, Nov 24, 2015, 19:29 Glasser, Matthew <glass...@wustl.edu 
> <mailto:glass...@wustl.edu>> wrote:
> I’m still not following why it matters.
> 
> Peace,
> 
> Matt.
> 
> From: Mary Beth <m...@jhmi.edu <mailto:m...@jhmi.edu>>
> Date: Tuesday, November 24, 2015 at 6:18 PM
> To: Matt Glasser <glass...@wustl.edu <mailto:glass...@wustl.edu>>, 
> "hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>" 
> <hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>>
> Subject: Re: [HCP-Users] phase encoding and group ICA
> 
> I just want to make sure I'm comparing apples to apples when I use the 
> subject-specific timeseries. 
> 
> best,
> mb
> 
> On Tue, Nov 24, 2015 at 7:11 PM Glasser, Matthew <glass...@wustl.edu 
> <mailto:glass...@wustl.edu>> wrote:
> Why does the order of the individual subject sessions matter for group ICA or 
> PTNs?
> 
> Peace,
> 
> Matt.
> 
> From: <hcp-users-boun...@humanconnectome.org 
> <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Mary Beth 
> <m...@jhmi.edu <mailto:m...@jhmi.edu>>
> Date: Tuesday, November 24, 2015 at 5:59 PM
> To: "hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>" 
> <hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>>
> Subject: [HCP-Users] phase encoding and group ICA
> 
> Hi all,
> 
> According to this page 
> http://www.humanconnectome.org/documentation/Q1/data-in-this-release.html 
> <http://www.humanconnectome.org/documentation/Q1/data-in-this-release.html>, 
> prior to 1 October 2012, the first resting state session of each visit was 
> acquired with RL phase encoding, and the second session was acquired with LR 
> phase encoding (RL/LR).  After this date, the first visit continued to be 
> acquired in the RL/LR order, but the second visit was acquired in the 
> opposite order, with the LR acquisition followed by the RL acquisition 
> (LR/RL). 
> 
> Here's my question: prior to group ICA and the generation of subject-specific 
> sets of node timeseries in the August, 2014 “HCP500-PTN” 
> (Parcellation+Timeseries+Netmats) data release, were the sessions for 
> subjects acquired before 1 October 2012 reordered to match the order of 
> sessions for subjects acquired after 1 October 2012?
> 
> Thanks in advance,
> Mary Beth
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org>
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users 
> <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, 
>