Re: [HCP-Users] aliasing in diffusion images

[Mark A. Pinsk]

Excite pulse duration: 2560 us
Refocus pulse duration: 5120 us
Single band images: off
MB LeakBlock Kernel: off
MB RF phase scramble: off
Time-shifted MB RF: off
SENSE1 coil combine: ON
Log physiology to file: off
Invert RO/PE polarity: off
Online multi-band recon: Online
FFT scale factor: 1.00



On Mon, Nov 23, 2015 at 6:29 PM, Harms, Michael  wrote:

>
> What are your settings on all the parameters on the Sequence:Special tab?
>
> --
> 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: "Mark A. Pinsk" 
> Date: Monday, November 23, 2015 10:39 AM
> To: "hcp-users@humanconnectome.org" 
> Subject: [HCP-Users] aliasing in diffusion images
>
> Hi all,
>
> I've attempted to collect diffusion data with the CMRR sequence at our
> Prisma, and got aliasing in the image (very apparent at higher b value).
> Snapshot here:
> https://dl.dropboxusercontent.com/u/3889124/b2500-MB3.tiff
>
> Any suggestions on what the issue(s) could be?
> I see the same when I lower MB from 3 to 2.
>
> Here are my protocol parameters:
> 64-channel head/neck coil
> 90 interleaved transverse slices
> in-plane resolution = 1.5mm
> slice thickness = 1.5mm with no inter-slice gap
> field of view (FOV) = 210mm
> base resolution = 140
> repetition time (TR) = 4200ms
> echo time (TE) = 87ms
> flip angle (FA) = 78 deg
> refocus FA = 160 deg
> phase partial fourier (PPF) = 6/8
> gradient reversed fat suppression
> phase encode (PE) direction = anterior/posterior
> bandwidth = 1880Hz/Px
> echo spacing (ES) = 0.71ms
> multiband acceleration factor = 3
> SENSE (R=1) image reconstruction
> bmax = 2500 s/mm^2
>
>
> thanks!
> Mark
>
> ___
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>
>
> --
>
> 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] aliasing in diffusion images

[Harms, Michael]

What are your settings on all the parameters on the Sequence:Special tab?




-- 
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: "Mark A. Pinsk" 
Date: Monday, November 23, 2015 10:39 AM
To: "hcp-users@humanconnectome.org" 
Subject: [HCP-Users] aliasing in diffusion images





Hi all,


I've attempted to collect diffusion data with the CMRR sequence at our Prisma, and got aliasing in the image (very apparent at higher b value).  Snapshot here:  
https://dl.dropboxusercontent.com/u/3889124/b2500-MB3.tiff



Any suggestions on what the issue(s) could be?  
I see the same when I lower MB from 3 to 2.


Here are my protocol parameters:
64-channel head/neck coil
90 interleaved transverse slices
in-plane resolution = 1.5mm
slice thickness = 1.5mm with no inter-slice gap
field of view (FOV) = 210mm
base resolution = 140
repetition time (TR) = 4200ms
echo time (TE) = 87ms
flip angle (FA) = 78 deg
refocus FA = 160 deg
phase partial fourier (PPF) = 6/8
gradient reversed fat suppression
phase encode (PE) direction = anterior/posterior
bandwidth = 1880Hz/Px
echo spacing (ES) = 0.71ms
multiband acceleration factor = 3
SENSE (R=1) image reconstruction

bmax = 2500 s/mm^2




thanks!
Mark



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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] Phase Encoding left-to-right and right-to-left

[Glasser, Matthew]

It doesn't matter what order you concatenate the data in, but I would not 
recommend only analyzing the data of one phase encoding direction.

Peace,

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Joelle Zimmermann 
mailto:joelle.t.zimmerm...@gmail.com>>
Date: Monday, November 23, 2015 at 12:48 PM
To: "Elam, Jennifer" mailto:e...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Phase Encoding left-to-right and right-to-left

Hi Jennifer and Matt,

Thanks for your help. I have a few clarification questions below:
Does it matter in which order I concatenate the LR and the RL .nii's? My 
ultimate goal is to create a functional connectivity matrix from the time 
series.
#3 in the link you sent describes that there are 4 runs per subject. Is this 
the REST 1, and REST 2, each with LR and RL phase encoding directions?
Would using only one phase encoding direction (i.e. do analysis on LR) expect 
to effect the results?

Thanks,
Joelle

On Mon, Nov 23, 2015 at 1:17 PM, Jennifer Elam 
mailto:el...@pcg.wustl.edu>> wrote:
#3 on https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ may be 
of help.

Best,
Jenn

Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
el...@pcg.wustl.edu
www.humanconnectome.org

From:hcp-users-boun...@humanconnectome.org
 
[mailto:hcp-users-boun...@humanconnectome.org]
 On Behalf Of Glasser, Matthew
Sent: Monday, November 23, 2015 12:16 PM
To: Joelle Zimmermann; 
hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Phase Encoding left-to-right and right-to-left


Usually you concatenate them temporally after demeaning (and perhaps variance 
normalizing).



Peace,



Matt.


From:hcp-users-boun...@humanconnectome.org
 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Joelle Zimmermann 
mailto:joelle.t.zimmerm...@gmail.com>>
Sent: Monday, November 23, 2015 11:33 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Phase Encoding left-to-right and right-to-left

Hi all,

Would anyone be able to explain a bit more about the phase-encoding directions 
LR and RL for the (preprocessed) REST1 session data from 500 subjects +MEG2? I 
understand that LR is left to right and RL is right to left.

I'm wondering, are these meant to be somehow combined, or is only one of these 
typically chosen?

Thanks,
Joelle


http://www.humanconnectome.org/documentation/Q1/data-in-this-release.html
Q1 Data Release: About the Dataset | Human Connectome Project
76 healthy adult subjects in the age range 22 - 35 participated in the first 
quarter of data collection. These include 68 subjects with data from all or 
nearly all ...
Read 
more...



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Re: [HCP-Users] Is proprietary aspera browser plugin the only way to download the HCP Open data?

[Yizhou Ma]

Hi Kevin,

It's been more than two years and I am wondering if there has been any
updates for downloading the HCP data via command line?

Thanks,
Cherry

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Re: [HCP-Users] Trying to read HCP_S500_R468_MIGPd4500ROW.dconn.nii

[Timothy Coalson]

To get a dconn loaded in matlab, you of course need to have a large amount
of available memory.  Freezing is what I would expect if you don't have
enough memory, and start using a lot of swap space (some ways of loading
might initially load it as double precision, and need twice the memory).

As you mention specifically c++ as your end goal, have a look at CiftiLib,
as it is a c++ library for reading and writing cifti files, and has better
support and features than currently available matlab cifti reading/writing
(for instance, on disk reading/writing (not reading the entire file into
memory first), easy construction and full support of dimension mappings of
all supported types):

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

Tim


On Mon, Nov 23, 2015 at 11:18 AM, David Dalmazzo  wrote:

> Hello,
> I work in Specs Lab in Pompeu Fabra University as a Phd student.
> I'm building an app for connectome visualisation and brain activity
> simulation called BrainX3. The first version use Hagmann dataset based on
> 998 nodes and ~14.000 bidirectional connections.
>
> For the new version I would like to use HCP S500 dataset. My main problem
> is that following this two options about How to get CIFTI files into
> MATLAB, I don't find the solution. The first way using fieldTrip gives me
> some errors, but I'm already in contact with Robert Oostenveld who is
> helping me. And the second option using Gifti+wb_command, just crash/freeze
> my computer.
>
>
> https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-2.HowdoyougetCIFTIfilesintoMATLAB
> ?
>
> My question is how is the best way to extract the data, maybe I'm just
> missing a tutorial where it's well explained?
> My main purpose is to build an app in C++ of connectome visualization with
> much more resolution than Hagmann's.
>
> Right now I'm in OS X 10.11.1 and Matlab R2015b (8.6.0.267246) 64-bit.
>
> Thanks for the support,
>
> David
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

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Re: [HCP-Users] Convert NIFTI to CIFTI

[Donna Dierker]

Yes, I have, like so:

wb_command -cifti-convert -from-nifti ${NiftiIn} ${CiftiTemplate} ${CiftiOut} 
-reset-scalars

But not in the context you describe.  I was using randomise to generate group 
permuted t-maps and then bring them back to cifti before doing TFCE on the 
surface.  (Now I use PALM for that: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM)


On Nov 23, 2015, at 1:03 PM, Joe Borrello  wrote:

> Hi, I'm a PhD student just getting started on a project that involves 
> analyzing some data from the 500 subjects release and wanted to know if 
> anyone has had any experience using the -cifti-convert -from-nifti operations 
> to make cifti files. Ultimately, the goal is to compare test-retest 
> variability in myelin maps using the T1w/T2w method and the means of 
> comparison I was aiming to do would involved cifti-math.
> 
> Thanks in advance,
> Joe Borrello
> -- 
> Joseph Borrello
> 
> CEO & Co-Founder, Dynami-Cal Inc.
> 
> Biomedical Engineer, MSIT Rapid Prototyping Center
> 
> Research Assistant, Mount Sinai TMII
> 
> PhD Candidate, ISMMS
> 
> josephborrello.com
> 
> dynami-cal.com
> 
> msit.mssm.edu
> 
> ___
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> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> 


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Re: [HCP-Users] Convert NIFTI to CIFTI

[Timothy Coalson]

The -cift-convert command is only files that are organized the way cifti is
- the data in question has to have already been in cifti space before using
the command will do anything for you.  The nifti files written and accepted
by the command are "fake" nifti files, they only superficially resemble
volume files in their header info, they will not display meaningfully as a
volume.

If what you have is nifti volume files, then you will want to use commands
like -volume-to-surface-mapping and -cifti-create-dense-from-template (if
you already have a good surface registration) or
-cifti-create-dense-timeseries .  You may want to make use of the HCP
pipelines to do many of these steps for you.

Alternatively, if you are only doing math within a subject (not across
subjects), then the -volume-math command may do what you want.

Tim


On Mon, Nov 23, 2015 at 1:03 PM, Joe Borrello  wrote:

> Hi, I'm a PhD student just getting started on a project that involves
> analyzing some data from the 500 subjects release and wanted to know if
> anyone has had any experience using the *-cifti-convert -from-nifti 
> *operations
> to make cifti files. Ultimately, the goal is to compare test-retest
> variability in myelin maps using the T1w/T2w method and the means of
> comparison I was aiming to do would involved cifti-math.
>
> Thanks in advance,
> Joe Borrello
> --
>
> Joseph Borrello
>
> CEO & Co-Founder, Dynami-Cal Inc.
>
> Biomedical Engineer, MSIT Rapid Prototyping Center
>
> Research Assistant, Mount Sinai TMII
>
> PhD Candidate, ISMMS
>
> josephborrello.com
>
> dynami-cal.com
>
> msit.mssm.edu
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

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Re: [HCP-Users] Tractography on diffusion data for SC matrices

[Jennifer Elam]

Hi Joelle and all,

HCP does have running bedpostX on the diffusion data for HCP Subjects on our to 
do list, but this data has not been released yet. We are hoping to have this 
available to users by late winter/early spring 2016 after we release 7T data.

 

Best,

Jenn

 

Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
  314-362-9387
  el...@pcg.wustl.edu
  www.humanconnectome.org

 

From: Joelle Zimmermann [mailto:joelle.t.zimmerm...@gmail.com] 
Sent: Monday, November 23, 2015 12:54 PM
To: Jennifer Elam; hcp-users@humanconnectome.org
Subject: Tractography on diffusion data for SC matrices

 

Hi Jennifer,

 

I previously posted a question to the mailing list, and wanted to check with 
you as you may have a bit more of an insiders scoop.

 

I was wondering whether tractography has been performed on the diffusion data 
for the end of creating structural connectivity matrices for individual 
subjects; or something that is in the plans?  I would expect this is something 
that would be of interest to quite a few people, and would definitely be of a 
lot of use to me.

 

Thanks,

Joelle


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[HCP-Users] Convert NIFTI to CIFTI

[Joe Borrello]

Hi, I'm a PhD student just getting started on a project that involves
analyzing some data from the 500 subjects release and wanted to know if
anyone has had any experience using the *-cifti-convert -from-nifti *operations
to make cifti files. Ultimately, the goal is to compare test-retest
variability in myelin maps using the T1w/T2w method and the means of
comparison I was aiming to do would involved cifti-math.

Thanks in advance,
Joe Borrello
-- 

Joseph Borrello

CEO & Co-Founder, Dynami-Cal Inc.

Biomedical Engineer, MSIT Rapid Prototyping Center

Research Assistant, Mount Sinai TMII

PhD Candidate, ISMMS

josephborrello.com

dynami-cal.com

msit.mssm.edu

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[HCP-Users] Tractography on diffusion data for SC matrices

[Joelle Zimmermann]

Hi Jennifer,

I previously posted a question to the mailing list, and wanted to check
with you as you may have a bit more of an insiders scoop.

I was wondering whether tractography has been performed on the diffusion
data for the end of creating structural connectivity matrices for
individual subjects; or something that is in the plans?  I would expect
this is something that would be of interest to quite a few people, and
would definitely be of a lot of use to me.

Thanks,
Joelle

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Re: [HCP-Users] Phase Encoding left-to-right and right-to-left

[Joelle Zimmermann]

Hi Jennifer and Matt,

Thanks for your help. I have a few clarification questions below:
Does it matter in which order I concatenate the LR and the RL .nii's? My
ultimate goal is to create a functional connectivity matrix from the time
series.
#3 in the link you sent describes that there are 4 runs per subject. Is
this the REST 1, and REST 2, each with LR and RL phase encoding directions?
Would using only one phase encoding direction (i.e. do analysis on LR)
expect to effect the results?

Thanks,
Joelle

On Mon, Nov 23, 2015 at 1:17 PM, Jennifer Elam  wrote:

> #3 on https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ
> may be of help.
>
>
>
> Best,
>
> Jenn
>
>
>
> Jennifer Elam, Ph.D.
> Outreach Coordinator, Human Connectome Project
> Washington University School of Medicine
> Department of Anatomy and Neurobiology, Box 8108
> 660 South Euclid Avenue
> St. Louis, MO 63110
> 314-362-9387
> el...@pcg.wustl.edu
> www.humanconnectome.org
>
>
>
> *From:* hcp-users-boun...@humanconnectome.org [mailto:
> hcp-users-boun...@humanconnectome.org] *On Behalf Of *Glasser, Matthew
> *Sent:* Monday, November 23, 2015 12:16 PM
> *To:* Joelle Zimmermann; hcp-users@humanconnectome.org
> *Subject:* Re: [HCP-Users] Phase Encoding left-to-right and right-to-left
>
>
>
> Usually you concatenate them temporally after demeaning (and perhaps
> variance normalizing).
>
>
>
> Peace,
>
>
>
> Matt.
>
>
> --
>
> *From:* hcp-users-boun...@humanconnectome.org <
> hcp-users-boun...@humanconnectome.org> on behalf of Joelle Zimmermann <
> joelle.t.zimmerm...@gmail.com>
> *Sent:* Monday, November 23, 2015 11:33 AM
> *To:* hcp-users@humanconnectome.org
> *Subject:* [HCP-Users] Phase Encoding left-to-right and right-to-left
>
>
>
> Hi all,
>
>
>
> Would anyone be able to explain a bit more about the phase-encoding
> directions LR and RL for the (preprocessed) REST1 session data from 500
> subjects +MEG2? I understand that LR is left to right and RL is right to
> left.
>
>
>
> I'm wondering, are these meant to be somehow combined, or is only one of
> these typically chosen?
>
>
>
> Thanks,
>
> Joelle
>
>
>
>
>
> http://www.humanconnectome.org/documentation/Q1/data-in-this-release.html
>
> Q1 Data Release: About the Dataset | Human Connectome Project
>
> 76 healthy adult subjects in the age range 22 – 35 participated in the
> first quarter of data collection. These include 68 subjects with data from
> all or nearly all ...
>
> Read more...
> 
>
>
>
> ___
> 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
>

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Re: [HCP-Users] Trying to read HCP_S500_R468_MIGPd4500ROW.dconn.nii

[David Dalmazzo]

Hi Matt,
This file is HCP_S500_R468_MIGPd4500ROW.dconn.nii (33GB). But right now it
is working with the last updated version of fieldtrip.
Thanks for the support anyway

David

On Mon, Nov 23, 2015 at 7:14 PM, Glasser, Matthew 
wrote:

> What CIFTI data are you trying to get into matlab?
>
>
> Peace,
>
>
> Matt.
>
>
> --
> *From:* hcp-users-boun...@humanconnectome.org <
> hcp-users-boun...@humanconnectome.org> on behalf of David Dalmazzo <
> davm...@gmail.com>
> *Sent:* Monday, November 23, 2015 11:18 AM
> *To:* hcp-users@humanconnectome.org
> *Subject:* [HCP-Users] Trying to read HCP_S500_R468_MIGPd4500ROW.dconn.nii
>
> Hello,
> I work in Specs Lab in Pompeu Fabra University as a Phd student.
> I'm building an app for connectome visualisation and brain activity
> simulation called BrainX3. The first version use Hagmann dataset based on
> 998 nodes and ~14.000 bidirectional connections.
>
> For the new version I would like to use HCP S500 dataset. My main problem
> is that following this two options about How to get CIFTI files into
> MATLAB, I don't find the solution. The first way using fieldTrip gives me
> some errors, but I'm already in contact with Robert Oostenveld who is
> helping me. And the second option using Gifti+wb_command, just crash/freeze
> my computer.
>
>
> https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-2.HowdoyougetCIFTIfilesintoMATLAB
> ?
>
> My question is how is the best way to extract the data, maybe I'm just
> missing a tutorial where it's well explained?
> My main purpose is to build an app in C++ of connectome visualization with
> much more resolution than Hagmann's.
>
> Right now I'm in OS X 10.11.1 and Matlab R2015b (8.6.0.267246) 64-bit.
>
> Thanks for the support,
>
> David
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

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Re: [HCP-Users] Phase Encoding left-to-right and right-to-left

[Jennifer Elam]

#3 on https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ may
be of help.

 

Best,

Jenn

 

Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
el...@pcg.wustl.edu
www.humanconnectome.org

 

From: hcp-users-boun...@humanconnectome.org
[mailto:hcp-users-boun...@humanconnectome.org] On Behalf Of Glasser, Matthew
Sent: Monday, November 23, 2015 12:16 PM
To: Joelle Zimmermann; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Phase Encoding left-to-right and right-to-left

 

Usually you concatenate them temporally after demeaning (and perhaps
variance normalizing).

 

Peace,

 

Matt.

 

  _  

From: hcp-users-boun...@humanconnectome.org
 on behalf of Joelle Zimmermann

Sent: Monday, November 23, 2015 11:33 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Phase Encoding left-to-right and right-to-left 

 

Hi all,

 

Would anyone be able to explain a bit more about the phase-encoding
directions LR and RL for the (preprocessed) REST1 session data from 500
subjects +MEG2? I understand that LR is left to right and RL is right to
left. 

 

I'm wondering, are these meant to be somehow combined, or is only one of
these typically chosen?

 

Thanks,

Joelle

 

 

http://www.humanconnectome.org/documentation/Q1/data-in-this-release.html 


Q1 Data Release: About the Dataset | Human Connectome Project

76 healthy adult subjects in the age range 22 - 35 participated in the first
quarter of data collection. These include 68 subjects with data from all or
nearly all ...

 
Read more...

 

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Re: [HCP-Users] Phase Encoding left-to-right and right-to-left

[Glasser, Matthew]

Usually you concatenate them temporally after demeaning (and perhaps variance 
normalizing).


Peace,


Matt.


From: hcp-users-boun...@humanconnectome.org 
 on behalf of Joelle Zimmermann 

Sent: Monday, November 23, 2015 11:33 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Phase Encoding left-to-right and right-to-left

Hi all,

Would anyone be able to explain a bit more about the phase-encoding directions 
LR and RL for the (preprocessed) REST1 session data from 500 subjects +MEG2? I 
understand that LR is left to right and RL is right to left.

I'm wondering, are these meant to be somehow combined, or is only one of these 
typically chosen?

Thanks,
Joelle


http://www.humanconnectome.org/documentation/Q1/data-in-this-release.html
Q1 Data Release: About the Dataset | Human Connectome Project
76 healthy adult subjects in the age range 22 - 35 participated in the first 
quarter of data collection. These include 68 subjects with data from all or 
nearly all ...
Read 
more...




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Re: [HCP-Users] Trying to read HCP_S500_R468_MIGPd4500ROW.dconn.nii

[Glasser, Matthew]

What CIFTI data are you trying to get into matlab?

Peace,


Matt.



From: hcp-users-boun...@humanconnectome.org 
 on behalf of David Dalmazzo 

Sent: Monday, November 23, 2015 11:18 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Trying to read HCP_S500_R468_MIGPd4500ROW.dconn.nii

Hello,
I work in Specs Lab in Pompeu Fabra University as a Phd student.
I'm building an app for connectome visualisation and brain activity simulation 
called BrainX3. The first version use Hagmann dataset based on 998 nodes and 
~14.000 bidirectional connections.

For the new version I would like to use HCP S500 dataset. My main problem is 
that following this two options about How to get CIFTI files into MATLAB, I 
don't find the solution. The first way using fieldTrip gives me some errors, 
but I'm already in contact with Robert Oostenveld who is helping me. And the 
second option using Gifti+wb_command, just crash/freeze my computer.

https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-2.HowdoyougetCIFTIfilesintoMATLAB?

My question is how is the best way to extract the data, maybe I'm just missing 
a tutorial where it's well explained?
My main purpose is to build an app in C++ of connectome visualization with much 
more resolution than Hagmann's.

Right now I'm in OS X 10.11.1 and Matlab R2015b (8.6.0.267246) 64-bit.

Thanks for the support,

David

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[HCP-Users] Phase Encoding left-to-right and right-to-left

[Joelle Zimmermann]

Hi all,

Would anyone be able to explain a bit more about the phase-encoding
directions LR and RL for the (preprocessed) REST1 session data from 500
subjects +MEG2? I understand that LR is left to right and RL is right to
left.

I'm wondering, are these meant to be somehow combined, or is only one of
these typically chosen?

Thanks,
Joelle


http://www.humanconnectome.org/documentation/Q1/data-in-this-release.html

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[HCP-Users] Trying to read HCP_S500_R468_MIGPd4500ROW.dconn.nii

[David Dalmazzo]

Hello,
I work in Specs Lab in Pompeu Fabra University as a Phd student.
I'm building an app for connectome visualisation and brain activity
simulation called BrainX3. The first version use Hagmann dataset based on
998 nodes and ~14.000 bidirectional connections.

For the new version I would like to use HCP S500 dataset. My main problem
is that following this two options about How to get CIFTI files into
MATLAB, I don't find the solution. The first way using fieldTrip gives me
some errors, but I'm already in contact with Robert Oostenveld who is
helping me. And the second option using Gifti+wb_command, just crash/freeze
my computer.

https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-2.HowdoyougetCIFTIfilesintoMATLAB
?

My question is how is the best way to extract the data, maybe I'm just
missing a tutorial where it's well explained?
My main purpose is to build an app in C++ of connectome visualization with
much more resolution than Hagmann's.

Right now I'm in OS X 10.11.1 and Matlab R2015b (8.6.0.267246) 64-bit.

Thanks for the support,

David

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[HCP-Users] aliasing in diffusion images

[Mark A. Pinsk]

Hi all,

I've attempted to collect diffusion data with the CMRR sequence at our
Prisma, and got aliasing in the image (very apparent at higher b value).
Snapshot here:
https://dl.dropboxusercontent.com/u/3889124/b2500-MB3.tiff

Any suggestions on what the issue(s) could be?
I see the same when I lower MB from 3 to 2.

Here are my protocol parameters:
64-channel head/neck coil
90 interleaved transverse slices
in-plane resolution = 1.5mm
slice thickness = 1.5mm with no inter-slice gap
field of view (FOV) = 210mm
base resolution = 140
repetition time (TR) = 4200ms
echo time (TE) = 87ms
flip angle (FA) = 78 deg
refocus FA = 160 deg
phase partial fourier (PPF) = 6/8
gradient reversed fat suppression
phase encode (PE) direction = anterior/posterior
bandwidth = 1880Hz/Px
echo spacing (ES) = 0.71ms
multiband acceleration factor = 3
SENSE (R=1) image reconstruction
bmax = 2500 s/mm^2


thanks!
Mark

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