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> 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> 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 <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
>>>>
>>>> Tim
>>>>
>>>>
>>>> On Mon, Nov 23, 2015 at 11:18 AM, David Dalmazzo <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
>>>>> ?
>>>>>
>>>>> 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
>>>>>
>>>>
>>>> _______________________________________________
>>>> HCP-Users mailing list
>>>> HCP-Users@humanconnectome.org
>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>>
>>>
>>>
>>
>
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