One should note that the answer from using such an operation on the cifti
matrix will be in cifti indices, so if you want to get them as voxel and
vertex indices, you will need some additional information. The
-cifti-export-dense-mapping command may be helpful here.
Additionally, thanks to Robert Oostenveld, there is now a matlab cifti
reader available that parses the cifti xml, which should provide the brain
models ("dense") mapping information, available here:
https://github.com/Washington-University/cifti-matlab
Tim
On Tue, Jan 6, 2015 at 4:12 PM, Harms, Michael <[email protected]> wrote:
>
> If you are willing to use 'matlab', another option is to load the
> dlabel.nii into matlab, and then using the FIND command you can easily get
> a list of all the indices corresponding to a given (numeric) label ID.
>
> 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 63110 Email: [email protected]
>
> From: Timothy Coalson <[email protected]>
> Date: Tuesday, January 6, 2015 3:57 PM
> To: Oscar Miranda Dominguez <[email protected]>
> Cc: "[email protected]" <[email protected]>
> Subject: Re: [HCP-Users] List of grayordinates belonging to each
> ROI-cifti parcellate
>
> In the dlabel.nii file, this information is in the data matrix, not the
> header. One way to get this information is from the header of a
> ptseries.nii file (or other parcellated file type) resulting from
> parcellating with it. The -file-information command should report the
> counts of vertices ("nodes" which is terminology we used to use, next
> release this will say vertices) and voxels within each parcel, like so:
>
> ...
> ALONG_COLUMN map type: PARCELS
> Has Volume Data: false
> CortexLeft: 32492 nodes
> L_V1_ROI: Voxel-Count=0
> CortexLeft Node-Count=679
> L_MSTv_ROI: Voxel-Count=0
> CortexLeft Node-Count=40
> L_V6_ROI: Voxel-Count=0
> CortexLeft Node-Count=122
> L_V2_ROI: Voxel-Count=0
> CortexLeft Node-Count=731
> L_V3_ROI: Voxel-Count=0
> CortexLeft Node-Count=492
> ...
>
> In the Cifti XML (again, of the parcellated file, not the dlabel.nii),
> the lists you are looking for look like this:
>
> <MatrixIndicesMap AppliesToMatrixDimension="1"
> IndicesMapToDataType="CIFTI_INDEX_TYPE_PARCELS">
> <Surface BrainStructure="CIFTI_STRUCTURE_CORTEX_LEFT"
> SurfaceNumberOfVertices="32492"/>
> <Parcel Name="L_V1_ROI">
> <Vertices BrainStructure="CIFTI_STRUCTURE_CORTEX_LEFT">100
> 101 102 103 104 105 106 107 108 109 1489 1510 1530 1531 1549 1550 1567 1568
> 1569 1584 1585 1586 1600 1601 1615 23155 23156 23157 23158 23159 23160
> 23161 23162 23163 23164 23165 23166 23167 23168 23169 23170 23171 23172...
>
> There are some other ways to get the information (getting the dlabel.nii
> data and translating indices by the brain models map), but I think this is
> the closest to what you are asking without using additional tools.
>
> Tim
>
>
> On Tue, Jan 6, 2015 at 11:29 AM, Oscar Miranda Dominguez <
> [email protected]> wrote:
>
>> Hi
>>
>>
>>
>> I need some help with an easy issue!
>>
>> I have a few parcellations that I am using to make timecourses using
>> cifti-parcellate.
>>
>> However I am interested in knowing either of the following 2 thinks:
>>
>>
>>
>> 1. Which grayordinate belongs to each ROI, or
>>
>> 2. How many grayordinates belong to each ROI
>>
>>
>>
>> I know that this info should be in the label file. However, when I read
>> the header, I just see the list of ROIs and the ~32k grayordinates that
>> belong to each hemisphere.
>>
>> Any suggestions?
>>
>>
>>
>> Thanks in advance for your help and best regards!
>>
>>
>>
>> Oscar Miranda-Dominguez
>>
>> Postdoctoral Researcher
>>
>> Fair Neuroimaging Lab
>>
>> Phone: 503.418.1894 Fax: 503.494.9988
>>
>>
>>
>> Oregon Health and Science University
>>
>> Department of Behavioral Neuroscience
>>
>> *3181 SW Sam Jackson Park Road, L470*
>>
>> *Portland, OR 97239*
>>
>> http://www.ohsu.edu/fair-lab
>>
>>
>>
>> _______________________________________________
>> HCP-Users mailing list
>> [email protected]
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
>
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