Re: [HCP-Users] fMRISurface Pipeline FinalfMRIResolution Variable

[Glasser, Matthew]

What kind of resolution are we talking about?  The resolution parameters 
control the greyordinates space and the final volume space.

Peace,

Matt.

From: 
>
 on behalf of Timothy Coalson >
Date: Tuesday, August 29, 2017 at 5:44 PM
To: Timothy Hendrickson >
Cc: "hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] fMRISurface Pipeline FinalfMRIResolution Variable

I believe the pipelines generally expect isotropic resolution, yes.  I don't 
think there is currently a way to use that variable to represent a 
non-isotropic resolution.

However, there may be few (or no) steps that actually interpret that variable 
as a number and generate a new volume space using it, and instead it mostly 
just uses that string to look in the global/templates folder for matching 
filenames - if they happen to be non-isotropic, it would probably just use them.

Finally, though, the FinalfMRIResolution probably needs to match the CIFTI 
grayordinates space being used, and if you want to compare to HCP data, you 
need to eventually wind up in the 91282 grayordinates space, which specifies 
2mm isotropic voxels in MNI space.  You might as well do that upsampling early 
rather than late, so that you don't need to generate new pipeline templates.

Tim


On Tue, Aug 29, 2017 at 4:35 PM, Timothy Hendrickson 
> wrote:
HCP users,

I did some searching on the list and could not find an answer to my question, I 
apologize if I missed it. I am attempting to use the HCP preprocessing 
pipelines to processing resting state data which was acquired with a lower 
resolution than HCP.

I notice that the FinalfMRIResolution variable expects one number as input. I 
have two questions about this.

1. Is this in reference to one particular resolution direction (X,Y,Z), if so 
which one?
2. If the pipeline expects an isotropic acquisition, how does one enter in an 
anistropic acquisition?

Thanks!

Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Bioinformatics and Computational Biology M.S. Candidate
Office: 612-624-6441
Mobile: 507-259-3434 (texts okay)

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Re: [HCP-Users] fMRISurface Pipeline FinalfMRIResolution Variable

[Timothy Coalson]

I believe the pipelines generally expect isotropic resolution, yes.  I
don't think there is currently a way to use that variable to represent a
non-isotropic resolution.

However, there may be few (or no) steps that actually interpret that
variable as a number and generate a new volume space using it, and instead
it mostly just uses that string to look in the global/templates folder for
matching filenames - if they happen to be non-isotropic, it would probably
just use them.

Finally, though, the FinalfMRIResolution probably needs to match the CIFTI
grayordinates space being used, and if you want to compare to HCP data, you
need to eventually wind up in the 91282 grayordinates space, which
specifies 2mm isotropic voxels in MNI space.  You might as well do that
upsampling early rather than late, so that you don't need to generate new
pipeline templates.

Tim


On Tue, Aug 29, 2017 at 4:35 PM, Timothy Hendrickson 
wrote:

> HCP users,
>
> I did some searching on the list and could not find an answer to my
> question, I apologize if I missed it. I am attempting to use the HCP
> preprocessing pipelines to processing resting state data which was acquired
> with a lower resolution than HCP.
>
> I notice that the FinalfMRIResolution variable expects one number as
> input. I have two questions about this.
>
> 1. Is this in reference to one particular resolution direction (X,Y,Z), if
> so which one?
> 2. If the pipeline expects an isotropic acquisition, how does one enter in
> an anistropic acquisition?
>
> Thanks!
>
> Timothy Hendrickson
> Department of Psychiatry
> University of Minnesota
> Bioinformatics and Computational Biology M.S. Candidate
> Office: 612-624-6441 <(612)%20624-6441>
> Mobile: 507-259-3434 <(507)%20259-3434> (texts okay)
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

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Re: [HCP-Users] motion parameters

[Harms, Michael]

Hi,
We don’t have a single average head motion for each subject stored as a 
variable in ConnectomeDB.  You can find the average frame-to-frame motion for 
each fMRI run (rfMRI or tfMR) in the Movement_RelativeRMS_mean.txt file for 
that run.

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: Tuesday, August 29, 2017 at 5:16 PM
To: "hcp-users@humanconnectome.org" 
Subject: [HCP-Users] motion parameters

Hi HCPers,
I was wondering where I can find an average head motion parameter for each 
subject?
Thanks,
Joelle

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[HCP-Users] motion parameters

[Joelle Zimmermann]

Hi HCPers,

I was wondering where I can find an average head motion parameter for each
subject?

Thanks,
Joelle

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[HCP-Users] fMRISurface Pipeline FinalfMRIResolution Variable

[Timothy Hendrickson]

HCP users,

I did some searching on the list and could not find an answer to my
question, I apologize if I missed it. I am attempting to use the HCP
preprocessing pipelines to processing resting state data which was acquired
with a lower resolution than HCP.

I notice that the FinalfMRIResolution variable expects one number as input.
I have two questions about this.

1. Is this in reference to one particular resolution direction (X,Y,Z), if
so which one?
2. If the pipeline expects an isotropic acquisition, how does one enter in
an anistropic acquisition?

Thanks!

Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Bioinformatics and Computational Biology M.S. Candidate
Office: 612-624-6441
Mobile: 507-259-3434 (texts okay)

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