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 
(<some-directory-on-your-computer>/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 <davm...@gmail.com> 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 <tsc...@mst.edu 
> <mailto:tsc...@mst.edu>> 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 <davm...@gmail.com 
> <mailto:davm...@gmail.com>> 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 
> <mailto:mailboxofr...@gmail.com>> wrote:
> Thank you!
> 
> On Mon, Nov 23, 2015 at 3:03 PM, Timothy Coalson <tsc...@mst.edu 
> <mailto:tsc...@mst.edu>> 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 
> <https://github.com/Washington-University/CiftiLib>
> 
> Tim
> 
> 
> On Mon, Nov 23, 2015 at 11:18 AM, David Dalmazzo <davm...@gmail.com 
> <mailto:davm...@gmail.com>> 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
>  
> <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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