ectome.org>"
mailto:HCP-Users@humanconnectome.org>>, "Harms,
Michael" mailto:mha...@wustl.edu>>
Cc: Jennifer Elam mailto:jse...@gmail.com>>, Timothy Coalson
mailto:tsc...@mst.edu>>
Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI
Hi again, let m
Sunday, January 8, 2017 1:09 PM
To: Shearrer, Grace
Cc: Jennifer Elam; NEUROSCIENCE tim
Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI
Hi Grace,
Have a look at wb_command -cifti-help
Matt.
From: "Shearrer, Grace" mailto:grac...@email.unc.edu>>
Date: Sunday, Ja
> *Sent:* Wednesday, January 4, 2017 8:43 PM
>
> *To:* Shearrer, Grace
> *Cc:* Glasser, Matthew; Elam, Jennifer; aus...@gmail.com;
> HCP-Users@humanconnectome.org
> *Subject:* Re: [HCP-Users] Creating Group Average Resting State fMRI
>
> Not quite, you still need to do -cif
nifer; aus...@gmail.com;
HCP-Users@humanconnectome.org
Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI
Not quite, you still need to do -cifti-merge to concatenate across subjects to
get one matrix that reflects data from all subjects.
Per subject, with a little bit of pa
er, Grace
Cc: Glasser, Matthew; Elam, Jennifer;
aus...@gmail.com<mailto:aus...@gmail.com>;
HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI
Are you planning to concatenate the timeseries across all
ce
Cc: Glasser, Matthew; Elam, Jennifer;
aus...@gmail.com<mailto:aus...@gmail.com>;
HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI
Are you planning to concatenate the timeseries across all subjects
1 -repeat
>> 4) wb_command -cifit-merge
>> 5) wb_command -cifti-parcellate
>>
>> 6) wb_command -cifit-correlation
>>
>>
>> Grace
>> --
>> *From:* Glasser, Matthew
>> *Sent:* Wednesday, January 4, 2017 6:22 PM
&g
PM
To: Shearrer, Grace
Cc: Glasser, Matthew; Elam, Jennifer; aus...@gmail.com;
HCP-Users@humanconnectome.org
Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI
Are you planning to concatenate the timeseries across all subjects? If so, I
would suggest parcellating in each subject
Peace,
>
> Matt.
>
> From: "Shearrer, Grace"
> Date: Wednesday, January 4, 2017 at 4:16 PM
> To: Matt Glasser , "Elam, Jennifer" ,
> "aus...@gmail.com" , "HCP-Users@humanconnectome.org" <
> HCP-Users@humanconnectome.org>
> Subje
.com;
HCP-Users@humanconnectome.org
Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI
I would insert the parcellation between steps 5 and 6. The result if you use
the file I suggested below will be a 360 X 360 cortical area correlation matrix.
Peace,
Matt.
From: "
ustl.edu>>
Sent: Wednesday, January 4, 2017 5:54 PM
To: Elam, Jennifer; Shearrer, Grace; aus...@gmail.com<mailto:aus...@gmail.com>;
HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI
You will n
ectome.org
Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI
You will need to parcellate the data first using wb_command -cifti-parcellate.
A parcellation is available here:
https://balsa.wustl.edu/file/show/3VLx
Peace,
Matt.
From:
mailto:hcp-users-boun...@humanconnectome
ome.org/>
From: Shearrer, Grace mailto:grac...@email.unc.edu>>
Sent: Wednesday, January 4, 2017 2:16:48 PM
To: Elam, Jennifer; aus...@gmail.com<mailto:aus...@gmail.com>;
HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
Subjec
2:16:48 PM
To: Elam, Jennifer; aus...@gmail.com; HCP-Users@humanconnectome.org
Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI
?Hi Jenn, oops the User list verification was going to my junk email. I just
signed up though. I did see the wiki and it was helpful, I like this script
thoug
, Jennifer
Sent: Wednesday, January 4, 2017 4:57 PM
To: Shearrer, Grace; aus...@gmail.com; HCP-Users@humanconnectome.org
Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI
Hi Grace,
You might also want to check out the instructions for creating individual and
group average dense
2017 1:24:49 PM
To: aus...@gmail.com; HCP-Users@humanconnectome.org
Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI
Hi Dr. Bari,
thank you so much for script this is very helpful. I just want to check that I
understand. I would use your script to get the mean time series, standard
de
Hi Dr. Bari,
thank you so much for script this is very helpful. I just want to check that I
understand. I would use your script to get the mean time series, standard
deviation, and then demean the data. Then I would use a command like:
wb_command -cifit-merge
to then merge all my demeaned d
t; St. Louis, MO 63110 Email: mha...@wustl.edu
>
> From: Ausaf Bari
> Date: Tuesday, May 20, 2014 5:56 PM
> To: Matt Glasser
>
> Cc: "hcp-users@humanconnectome.org"
> Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI
>
> On a similar n
edu>
Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI
On a similar note, I also want to find the group average of a particular task fMRI such as the emotion task fMRI. I found a .dscalar.nii
t;
>>>> Demean and normalize functionality might be useful things to add to
>>>> wb_command -cifti-merge, unless there is a simple wb_command way to do this
>>>> already (we generally do this in matlab now).
>>>>
>>>> Matt.
>&
d average the connectomes across
> subjects). There will be a better way in the future.
>
> Peace,
>
> Matt.
>
> From: Timothy Coalson
> Date: Monday, May 19, 2014 at 10:48 PM
> To: Ausaf Bari
> Cc: "hcp-users@humanconnectome.org"
> Subject: Re: [
>> subjects? Is there any downside to this other than the huge amount of
>>>> storage space that would be required (32GB per subject)?
>>>>
>>>> -Ausaf
>>>>
>>>>
>>>> On Mon, May 19, 2014 at 10:04 PM, Glasser, Matthew <
&
ere is a simple wb_command way to do this
>>> already (we generally do this in matlab now).
>>>
>>> Matt.
>>>
>>> From: Timothy Coalson
>>> Date: Tuesday, May 20, 2014 at 12:19 PM
>>> To: Stephen Smith
>>> Cc: Ausaf Bari
; On Mon, May 19, 2014 at 10:04 PM, Glasser, Matthew <
>>> glass...@wusm.wustl.edu> wrote:
>>>
>>>> The simplest way is to concatenate the timeseries with wb_command
>>>> -cifti-merge. You could do this for all runs of all subjects, or all runs
>
" <
> hcp-users@humanconnectome.org>
>
> Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI
>
> Should you also normalize so that the standard deviations of each
> timeseries match?
>
> Tim
>
>
>
> On Tue, May 20, 2014 at 12:24 PM,
ephen Smith
> Cc: Ausaf Bari , "hcp-users@humanconnectome.org" <
> hcp-users@humanconnectome.org>
>
> Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI
>
> Should you also normalize so that the standard deviations of each
> timeseries match?
>
&
tephen Smith <st...@fmrib.ox.ac.uk>
Cc: Ausaf Bari <aus...@gmail.com>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI
Should you also normalize so that the standard deviations of each
>> From: Timothy Coalson
>> Date: Monday, May 19, 2014 at 10:48 PM
>> To: Ausaf Bari
>> Cc: "hcp-users@humanconnectome.org"
>> Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI
>>
>> Averaging together timepoints does not m
ter way in the future.
>
> Peace,
>
> Matt.
>
> From: Timothy Coalson
> Date: Monday, May 19, 2014 at 10:48 PM
> To: Ausaf Bari
> Cc: "hcp-users@humanconnectome.org"
> Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI
>
>
bjects). There will be a better way in the future.
>
> Peace,
>
> Matt.
>
> From: Timothy Coalson
> Date: Monday, May 19, 2014 at 10:48 PM
> To: Ausaf Bari
> Cc: "hcp-users@humanconnectome.org"
> Subject: Re: [HCP-Users] Creating Group Average Restin
: Timothy Coalson <tsc...@mst.edu>
Date: Monday, May 19, 2014 at 10:48 PM
To: Ausaf Bari <aus...@gmail.com>
Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI
Averaging together ti
Averaging together timepoints does not make sense for resting state data,
it does not use stimuli, so there is no temporal correspondence between
runs or across subjects. You should do the correlation before any
averaging.
I'm not sure what method our pipelines use, so I'll let someone else
respo
I am trying to create a resting state fMRI average over 10 subjects to view
in connectome workbench. For each HCP subject, I found the following 4
files:
rfMRI_REST1_RL_Atlas_hp2000_clean.dtseries.nii
rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii
rfMRI_REST2_RL_Atlas_hp2000_clean.dtseries.nii
rfM
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