[HCP-Users] How to extract time course for a volume voxel with MNI coordinate

[#LONG HONGQUAN#]

Hi HCP Team,


Thank you for all the great works that have been done. I am new doing research 
in this area and would like to ask a simple question:


How do I extract time course for a volume voxel with MNI coordinate from 
CIFTI-2 *dtseries.nii file?


I am currently using the function ft_read_cifti in cifti-matlab library, but 
the data I got does not match with the graph I got from the workbench view.


Also, it seems in workbench v8.3 we could still export the time series graphs, 
but I did not find this feature in workbench v1.1.1.


Could you give me some suggestions on how to extract the time course for a 
single volume if I already have the MNI and IJK coordinate? I prefer to use 
Matlab.


Thank you. I would really appreciate if you could provide me with some hints.


Best Regards,

Hongquan Long

School of Computer Engineering

Nanyang Technological University





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Re: [HCP-Users] How to extract time course for a volume voxel with MNI coordinate

[Timothy Coalson]

So, 2/3 of the spatial locations in HCP CIFTI files are not voxels, only
the cerebellum and subcortical structures are represented as voxels.  I'm
not all that familiar with the structure that ft_read_cifti returns, but it
should have the information needed to translate between data matrix indices
and voxel indices for the parts that are represented as voxels.

If all else fails, you could use wb_command -cifti-separate with
-volume-all to get all the voxel-represented parts in a nifti volume file.
There is also -cifti-export-dense-mapping, but those indices do not align
with ft_read_cifti, as ft_read_cifti adds NaN values to the data matrix
where surface vertices are excluded from the CIFTI file.  Using option B of
the FAQ entry at
https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-2.HowdoyougetCIFTIfilesintoMATLAB?
will load the matrix from cifti without altering the indices, but provides
no information in matlab about which matrix indices are which
vertices/voxels.

Tim


On Tue, Aug 25, 2015 at 10:06 AM, #LONG HONGQUAN# long0...@e.ntu.edu.sg
wrote:

 Hi HCP Team,


 Thank you for all the great works that have been done. I am new doing
 research in this area and would like to ask a simple question:


 How do I extract time course for a volume voxel with MNI coordinate from
 CIFTI-2 *dtseries.nii file?


 I am currently using the function ft_read_cifti in cifti-matlab library,
 but the data I got does not match with the graph I got from the workbench
 view.


 Also, it seems in workbench v8.3 we could still export the time
 series graphs, but I did not find this feature in workbench v1.1.1.


 Could you give me some suggestions on how to extract the time course for a
 single volume if I already have the MNI and IJK coordinate? I prefer to use
 Matlab.


 Thank you. I would really appreciate if you could provide me with some
 hints.


 Best Regards,

 Hongquan Long

 School of Computer Engineering

 Nanyang Technological University





 ___
 HCP-Users mailing list
 HCP-Users@humanconnectome.org
 http://lists.humanconnectome.org/mailman/listinfo/hcp-users


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