Exactly what Matt says, you do not need to transform the data.
Stam
On 8 Aug 2013, at 02:08, Glasser, Matthew wrote:
> Stam may be able to answer this better than me. I think what you would do is
> to provide probtrackx the native to MNI (and MNI to native) warps and use the
> MNI space 32k white surfaces and subcortical ROIs. Note that diffusion data
> is in structural "native" undistorted space space.
>
> Peace,
>
> Matt.
>
> From: Huang Su-Chun <claire0...@gmail.com>
> Date: Wednesday, August 7, 2013 6:40 PM
> To: Matt Glasser <glass...@wusm.wustl.edu>
> Cc: Timothy Coalson <tsc...@mst.edu>, "hcp-users@humanconnectome.org"
> <hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] Coordinate of CIFTI files
>
> Thank you very much for the answers, it helps a lot.
>
> What I want to do is to create dense connectome matrix (which mentioned in
> the paper "The minimal preprocessing pipelines for Human Connectome Project"
> ) based on probabilistic tractography from HCP diffusion data. In order to
> achieve the goal, I need to know the relationship between the coordinates of
> diffusion voxels and the node indices of the surfaces of structural images.
>
> Cheers,
>
> Su
>
>
> 2013/8/7 Glasser, Matthew <glass...@wusm.wustl.edu>
>> The CIFTI standard space is in MNI space (subcortical voxels). If you use
>> the surface
>> ${StudyFolder}/${SubjectID}/MNINonLinear/fsaverage_LR32k/${SubjectID}.${Hemisphere}.midthickness.32k_fs_LR.surf.gii,
>> then you will have surface coordinates in MNI space as well.
>>
>> As for the question about diffusion data, you're going to need to be more
>> specific because I don't know what you are trying to do.
>>
>> Peace,
>>
>> Matt.
>>
>> From: Timothy Coalson <tsc...@mst.edu>
>> Date: Wednesday, August 7, 2013 4:11 PM
>> To: Huang Su-Chun <claire0...@gmail.com>
>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> Subject: Re: [HCP-Users] Coordinate of CIFTI files
>>
>> The volume space that should be used to turn the indices into an XYZ
>> location is in the Volume XML element, which in cifti 1.0 is a child of the
>> Matrix element (ignore the "TransformedSpace" attribute, we don't use it or
>> set it to anything different depending on the space). The meaning of the
>> XYZ coordinates depends entirely on how the cifti file was generated - just
>> like any volume file, it is possible to set any coordinate system you want.
>> I believe the cifti files we release in the hcp data have voxels in MNI
>> space via FNIRT.
>>
>> For completeness, cifti files do not contain the surface coordinates, you
>> must get those from the relevant surface file (.surf.gii in the hcp data).
>>
>> Tim
>>
>>
>>
>> On Wed, Aug 7, 2013 at 3:47 PM, Huang Su-Chun <claire0...@gmail.com> wrote:
>>> Hello HCP teams,
>>>
>>> Thank you for all the hard works you did. I have some questions about the
>>> coordinate of CIFTI files.
>>> I read the online material and it mentioned that there are node index (for
>>> surface), voxel index (for volume), and an XYZ coordinate. My questions is
>>> that what space the voxel index is in? (ex: MNI or Talairach). In the
>>> other words, how to transfer the diffusion data from MNI space to the CIFTI
>>> nodes and volume space? Also, what's the XYZ coordinate means? Is it in
>>> Talairach space? Or individual's anatomy space?
>>>
>>> Thank you very much for answering these detailed questions,
>>>
>>> Su
>>>
>>> --
>>> Su-Chun Huang
>>> Research Scientist
>>> Integrated Brain Imaging Center
>>> Department of Radiology
>>> University of Washington
>>> Seattle, WA 98195
>>> phone: 206-687-0113
>>> _______________________________________________
>>> HCP-Users mailing list
>>> HCP-Users@humanconnectome.org
>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
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>
>
> --
> Su-Chun Huang
> Research Scientist
> Integrated Brain Imaging Center
> Department of Radiology
> University of Washington
> Seattle, WA 98195
> phone: 206-687-0113
>
>
> 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
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> please immediately notify the sender via telephone or return mail.
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