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]<mailto:[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<tel:503.418.1894> Fax: 503.494.9988<tel: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
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