In case you (or someone else) eventually want to know which vertices are
used, let me try to explain. That xml snippet you posted is part of a
brain models ("dense") map, not a parcellated map. You need to look at the
xml of the output file of -cifti-parcellate, not one of the input files.
Also, if you parcellate a dconn.nii, the output will have one parcellated
and one brain models map, so look at both MatrixIndicesMap elements.
I should have mentioned this earlier, the -nifti-information command with
-print-xml will print the cifti xml by itself.
Another way to go about this would be to use -cifti-separate to turn the
.dlabel.nii file into two label.gii files (and a nifti label file if
desired/applicable), where the indexes will be the surface vertex indices,
so you wouldn't need to translate from cifti indices.
Tim
On Tue, Jan 6, 2015 at 5:32 PM, Oscar Miranda Dominguez <[email protected]>
wrote:
> Thank you!
>
>
>
> wb_command -file-information *.ptseries.nii made it for me!
>
>
>
> However, for some reason (probably the way I made the label and xml
> files), the xml file is not listing the vertices per parcellated roi. It
> list them per hemisphere:
>
>
>
> </Volume>
>
> <BrainModel IndexOffset="0" IndexCount="32492"
> BrainStructure="CIFTI_STRUCTURE_CORTEX_LEFT"
> ModelType="CIFTI_MODEL_TYPE_SURFACE" SurfaceNumberOfVertices="32492">
>
> <VertexIndices>0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17
> 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42
> 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67
> 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92
> 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112
> 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131
> 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150
> 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169
> 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188
> 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207
> 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226
> 227 228 229 230 231 232 233 234
>
>
>
> Anyway, the count of vertices per parcellated roi is good enough for my
> purposes!
>
>
>
> Thank you very much and best regards
>
> OMD
>
>
>
> *From:* Timothy Coalson [mailto:[email protected]]
> *Sent:* Tuesday, January 06, 2015 1:58 PM
> *To:* Oscar Miranda Dominguez
> *Cc:* [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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