[HCP-Users] ASQ and SSAGA

2015-12-02 Thread Manousos Klados
Dear all,

I would like to ask about the ASQ and SSAGA instruments. In the website it
mentions that these datasets are open. However, when I go to the first
subject of 500 dataset I cannot find them, despite the fact that they are
completed. Could someone please help me on this issue?

Thank you very much in advance
Manousos
Manousos Klados, PhD
Max Planck Institute for Human Cognitive & Brain Sciences
Research Group of Neuroanatomy and Connectivity

Phone: +49(0)-341-9940-2507  <+49(0)-341-9940-2507>
Mobile: +49(0)-176-6988-1781
Email: kla...@cbs.mpg.de  
Website: http://www.mklados.com
Skype: mklados | Twitter: @mklados
Address: Stephanstraße 1a PC D-04103 Leipzig Germany

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

2015-12-02 Thread John Harwell
If you want to run wb_command (the command line program) from the terminal, you 
should execute the file “wb_command” contained in the distribution’s 
“bin_macosx64” directory 
(/workbench/bin_macosx64/wb_command). 

wb_command.app is an OS X Bundle (a directory that contains the program and 
related files).

John Harwell

> On Dec 2, 2015, at 6:43 AM, David Dalmazzo  wrote:
> 
> Hi,
> I'm trying to run wb_command.app on OSX 10.11.1 but the app doesn't respond 
> or the terminal. 
> I'm running on root:xnu-3247.10.11~1/RELEASE_X86_64 x86_64  
> Do I miss a first step?
> Thanks for the help
> 
> David
> 
> On Wed, Nov 25, 2015 at 12:00 AM, Timothy Coalson  > wrote:
> This part of your call:
> 
> , 'readdata', false);
> 
> is telling ft_read_cifti to not load the data matrix, that is why it isn't 
> there.
> 
> If you are just as comfortable in C++, then yes, CiftiLib is likely the best 
> solution, it is directly based on the code we use in connectome workbench for 
> cifti files.  If what you need to do with the dconn organizes well with the 
> on-disk structure of the matrix (i.e., not needing more than a few rows in 
> memory at once, never needing to read columns), then it will work efficiently 
> with almost no memory footprint (as long as you don't tell it to read the 
> entire file into memory).
> 
> I don't think we distribute parcellated versions of the connectome yet, as 
> there hasn't exactly been a consensus on a parcellation for the entire 
> cortex.  You can use -cifti-parcellate to apply a parcellation to the dconn, 
> if you have one that you favor.
> 
> Tim
> 
> 
> On Tue, Nov 24, 2015 at 5:45 AM, David Dalmazzo  > wrote:
> Hello,
> With fieldTrip reading using this line 
> mycifti = 
> ft_read_cifti('/Users/David/Desktop/HumanConnectomeProject/HCP_S500_R468_rfMRI_MIGP_d4500ROW_zcorr/HCP_S500_R468_MIGPd4500ROW.dconn.nii',
>  'readdata', false);
> I get: dimond (pos_pos), hdr (1x1 struct), unit ('mm'), brain structure, 
> brainstructurelabel, dim, pos, transform. But the connectivity matrix is not 
> there.  
> 
> I'm going to check the C++ library. It seems to be the solution.
> Seems to be very difficult to work with this 33GB file. Is there in HCP 
> datasets any other file with connectome information, that have a connectivity 
> matrix or an array of region's connections? The Hagmann version seems to be 
> very old for the models we need to implement.
> 
> Thanks for the help
> David 
> 
>  
> 
> On Mon, Nov 23, 2015 at 9:14 PM, Rose Tharail John  > wrote:
> Thank you!
> 
> On Mon, Nov 23, 2015 at 3:03 PM, Timothy Coalson  > wrote:
> 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.
> 
> 

Re: [HCP-Users] ASQ and SSAGA

2015-12-02 Thread Jennifer Elam
Hi Manousos,

Access to the scores on the Achenbach Self Report and SSAGA psychiatric, life 
function and demographic measures are available only to those who have applied 
for and been granted access to the Restricted HCP data (see here 

 ). Because HCP is a twin family study we have had to put in extra safeguards 
to protect the privacy and anonymity of our subjects. 

 

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 Manousos Klados
Sent: Wednesday, December 02, 2015 4:57 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] ASQ and SSAGA

 

Dear all,

 

I would like to ask about the ASQ and SSAGA instruments. In the website it 
mentions that these datasets are open. However, when I go to the first subject 
of 500 dataset I cannot find them, despite the fact that they are completed. 
Could someone please help me on this issue? 

 

Thank you very much in advance

Manousos


Manousos Klados, PhD
Max Planck Institute for Human Cognitive & Brain Sciences
Research Group of Neuroanatomy and Connectivity

Phone:   +49(0)-341-9940-2507 
Mobile:   +49(0)-176-6988-1781
Email:   kla...@cbs.mpg.de 
Website:   http://www.mklados.com
Skype: mklados | Twitter: @mklados  
Address: Stephanstraße 1a PC D-04103 Leipzig Germany 

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Re: [HCP-Users] Transformation matrices of HCP 500 Subject Release

2015-12-02 Thread Harms, Michael

Hi,
You should be able to obtain the files via REST calls into the database.
See previous post in the list archives for an example of how to do so.

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  63110Email: mha...@wustl.edu




On 12/2/15 1:58 PM, "Kim, Joo-won"  wrote:

Dear HCP,

Thank you for the HCP data. I have a request.

Could you release the transformation matrices from unprocessed images to
ACPC aligned images of the HCP 500 Subjects Release? I would like to
analyze both averaged and individual scans, but when I ran the
PreFreeSurfer, the ACPC-aligned images were shifted a little bit compared
to those in the released data. Specifically, could you provide the
following files corresponding to the subjects in the attachment?

T1w/AverageT1wImages/ToHalfTrans000?.mat or
T1w/AverageT1wImages/ImToHalf000?.nii.gz
T1w/xfms/acpc.mat
T2w/AverageT2wImages/ToHalfTrans000?.mat or
T2w/AverageT2wImages/ImToHalf000?.nii.gz
T2w/xfms/acpc.mat
T2w/T2wToT1wReg/T2w2T1w.mat

Best,
Joo-won


--
Joo-won Kim

Postdoctoral Fellow
Translational and Molecular Imaging Institute
Department of Radiology
Icahn School of Medicine at Mount Sinai

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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 
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[HCP-Users] Transformation matrices of HCP 500 Subject Release

2015-12-02 Thread Kim, Joo-won
Dear HCP,

Thank you for the HCP data. I have a request.

Could you release the transformation matrices from unprocessed images to ACPC 
aligned images of the HCP 500 Subjects Release? I would like to analyze both 
averaged and individual scans, but when I ran the PreFreeSurfer, the 
ACPC-aligned images were shifted a little bit compared to those in the released 
data. Specifically, could you provide the following files corresponding to the 
subjects in the attachment?

T1w/AverageT1wImages/ToHalfTrans000?.mat or 
T1w/AverageT1wImages/ImToHalf000?.nii.gz
T1w/xfms/acpc.mat
T2w/AverageT2wImages/ToHalfTrans000?.mat or 
T2w/AverageT2wImages/ImToHalf000?.nii.gz
T2w/xfms/acpc.mat
T2w/T2wToT1wReg/T2w2T1w.mat

Best,
Joo-won


-- 
Joo-won Kim

Postdoctoral Fellow
Translational and Molecular Imaging Institute
Department of Radiology
Icahn School of Medicine at Mount Sinai

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100307
100408
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101915
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103414
103818
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899885


Re: [HCP-Users] Transformation matrices of HCP 500 Subject Release

2015-12-02 Thread Hodge, Michael

Joo-won,

We've recently created a "CREST" experiment for each released subject that 
should give you access to intermediate/non-relased files in the database via 
REST and for which you know the paths.

Here's an example for subject 100307 for one of the files you're interested in:

curl -s -k --cookie JSESSIONID=$DBSESSION 
https://db.humanconnectome.org/data/projects/HCP_500/subjects/100307/experiments/100307_CREST/resources/100307_CREST/files/T1w/AverageT1wImages/ImToHalf0001.nii.gz

The JSESSIONID variable can be set via the following:

DBSESSION=`curl -s -u username:password -X GET 
https://db.humanconnectome.org/data/JSESSIONID`;echo $DBSESSION

Regards,

Mike


From: hcp-users-boun...@humanconnectome.org 
 on behalf of Harms, Michael 

Sent: Wednesday, December 2, 2015 2:25 PM
To: Kim, Joo-won; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Transformation matrices of HCP 500 Subject Release

Hi,
You should be able to obtain the files via REST calls into the database.
See previous post in the list archives for an example of how to do so.

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  63110Email: mha...@wustl.edu




On 12/2/15 1:58 PM, "Kim, Joo-won"  wrote:

Dear HCP,

Thank you for the HCP data. I have a request.

Could you release the transformation matrices from unprocessed images to
ACPC aligned images of the HCP 500 Subjects Release? I would like to
analyze both averaged and individual scans, but when I ran the
PreFreeSurfer, the ACPC-aligned images were shifted a little bit compared
to those in the released data. Specifically, could you provide the
following files corresponding to the subjects in the attachment?

T1w/AverageT1wImages/ToHalfTrans000?.mat or
T1w/AverageT1wImages/ImToHalf000?.nii.gz
T1w/xfms/acpc.mat
T2w/AverageT2wImages/ToHalfTrans000?.mat or
T2w/AverageT2wImages/ImToHalf000?.nii.gz
T2w/xfms/acpc.mat
T2w/T2wToT1wReg/T2w2T1w.mat

Best,
Joo-won


--
Joo-won Kim

Postdoctoral Fellow
Translational and Molecular Imaging Institute
Department of Radiology
Icahn School of Medicine at Mount Sinai

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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 
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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 
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[HCP-Users] group-ICA spatial maps

2015-12-02 Thread Bagrat Amirikian
Hi,

 

I have downloaded and unpacked HCP500_Parcellation_Timeseries_Netmats data.
My question is about group ICA spatial maps, specifically, about
melodic_IC.dscalar.nii and melodic_IC_ftb.dlabel.nii files in the groupICA*
subdirectories. There is a very short description of these files in the
accompanying PDF file:

 

melodic_IC.dscalar.niiICA spatial maps (unthresholded
Zstats); one "timepoint" per map. Grayordinates

melodic_IC_ftb.dlabel.nii Summary "find the biggest" labels
image for all ICA spatial maps.  Grayordinates

 

I have loaded these files generated for 25-dimensional group-ICA to wb_view
with corresponding Q1-Q6_R440_midthikness surface files for their
inspection. 

 

1.   I can appreciate Zstats maps provided for each IC by
melodic_IC.dscalar.nii. How were exactly these Zstats computed? Are these
regular Z-scores obtained by subtracting the vertex/voxel-wise mean and
dividing by the standard deviation, or something else?

2.   When I click on the map and Information Window pops up, it shows
two SCALAR values for the selected vertex. For example:

 VERTEX CortexLeft: 28165
ANATOMICAL XYZ: -6.28827, 59.2204, -0.919904
CIFTI SCALARS melodic_IC.dscalar.nii: 0.935668 -0.20834

What do these two numbers 0.935668 and -0.20834 actually mean? I though
there should be just one number corresponding to the Zstat of the vertex.

3.   It appears that melodic_IC_ftb.dlabel.nii provides a hard
non-overlapping parcellation and labels each parcel (which could consist of
several spatially separated regions) by a color. The number of parcels
corresponds to the ICA dimension, 25 in this case.  How is this parcellation
obtained? How is the set of spatially continuous/diffusive maps of
individual ICs give rise to this parcellation with sharp non-overlapping
borders and without any gaps between the neighboring parcels?

 

Thank you very much for your help.

 

Bagrat

 

Bagrat Amirikian, Ph.D.

Department of Neuroscience

University of Minnesota Medical School

 

Brain Sciences Center

Minneapolis Veterans Affairs Health Care System


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

2015-12-02 Thread David Dalmazzo
Hi,
I'm trying to run wb_command.app on OSX 10.11.1 but the app doesn't respond
or the terminal.
I'm running on root:xnu-3247.10.11~1/RELEASE_X86_64 x86_64
Do I miss a first step?
Thanks for the help

David

On Wed, Nov 25, 2015 at 12:00 AM, Timothy Coalson  wrote:

> This part of your call:
>
> , 'readdata', false);
>
> is telling ft_read_cifti to not load the data matrix, that is why it isn't
> there.
>
> If you are just as comfortable in C++, then yes, CiftiLib is likely the
> best solution, it is directly based on the code we use in connectome
> workbench for cifti files.  If what you need to do with the dconn organizes
> well with the on-disk structure of the matrix (i.e., not needing more than
> a few rows in memory at once, never needing to read columns), then it will
> work efficiently with almost no memory footprint (as long as you don't tell
> it to read the entire file into memory).
>
> I don't think we distribute parcellated versions of the connectome yet, as
> there hasn't exactly been a consensus on a parcellation for the entire
> cortex.  You can use -cifti-parcellate to apply a parcellation to the
> dconn, if you have one that you favor.
>
> Tim
>
>
> On Tue, Nov 24, 2015 at 5:45 AM, David Dalmazzo  wrote:
>
>> Hello,
>> With fieldTrip reading using this line
>> mycifti = ft_read_cifti(
>> '/Users/David/Desktop/HumanConnectomeProject/HCP_S500_R468_rfMRI_MIGP_d4500ROW_zcorr/HCP_S500_R468_MIGPd4500ROW.dconn.nii',
>> 'readdata', false);
>> I get: dimond (pos_pos), hdr (1x1 struct), unit ('mm'), brain structure,
>> brainstructurelabel, dim, pos, transform. But the connectivity matrix is
>> not there.
>>
>> I'm going to check the C++ library. It seems to be the solution.
>> Seems to be very difficult to work with this 33GB file. Is there in HCP
>> datasets any other file with connectome information, that have a
>> connectivity matrix or an array of region's connections? The Hagmann
>> version seems to be very old for the models we need to implement.
>>
>> Thanks for the help
>> David
>>
>>
>>
>> On Mon, Nov 23, 2015 at 9:14 PM, Rose Tharail John <
>> mailboxofr...@gmail.com> wrote:
>>
>>> Thank you!
>>>
>>> On Mon, Nov 23, 2015 at 3:03 PM, Timothy Coalson  wrote:
>>>
 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
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> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

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>>>
>>>
>>
>

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