Freesurfer people,
I have a label file that I want to make into a volume file only in the white matter to use in diffusion tractography.
I was told to use mri_aparc2aseg to put the labels onto the WM surface and make them into a volume. I made the label files into annotation files using the following commands:
mris_label2annot --ctab clut.2lhV1.ctab --s 100206 --h lh --l /data/user/snolin/subjects_reconall/100206/label/2_LH_V1.label --a 2V1
mris_label2annot --ctab clut.2rhV1.ctab --s 100206 --h rh --l /data/user/snolin/subjects_reconall/100206/label/2_RH_V1.label --a 2V1
These ran with no errors and made annotation files. Then I ran mri_aparc2aseg using the following command:
mri_aparc2aseg --s 100206 --annot 2V1 --new-ribbon
This is my log file:
SUBJECTS_DIR /data/user/snolin/subjects_reconall
subject 100206
outvol /data/user/snolin/subjects_reconall/100206/mri/2V1+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0
Reading lh white surface
/data/user/snolin/subjects_reconall/100206/surf/lh.white
Reading lh pial surface
/data/user/snolin/subjects_reconall/100206/surf/lh.pial
Loading lh annotations from /data/user/snolin/subjects_reconall/100206/label/lh.2V1.annot
reading colortable from annotation file...
colortable with 2 entries read (originally clut.2lhV1.ctab)
Reading rh white surface
/data/user/snolin/subjects_reconall/100206/surf/rh.white
Reading rh pial surface
/data/user/snolin/subjects_reconall/100206/surf/rh.pial
Loading rh annotations from /data/user/snolin/subjects_reconall/100206/label/rh.2V1.annot
reading colortable from annotation file...
colortable with 2 entries read (originally clut.2rhV1.ctab)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /data/user/snolin/subjects_reconall/100206/mri/ribbon.mgz
Building hash of lh white
Building hash of lh pial
Building hash of rh white
Building hash of rh pial
Loading aseg from /data/user/snolin/subjects_reconall/100206/mri/aseg.mgz
ASeg Vox2RAS: -----------
-1.00000 0.00000 0.00000 128.00000;
0.00000 0.00000 1.00000 -128.00000;
0.00000 -1.00000 0.00000 128.00000;
0.00000 0.00000 0.00000 1.00000;
-------------------------
Labeling Slice
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
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 1764
Used brute-force search on 0 voxels
Writing output aseg to /data/user/snolin/subjects_reconall/100206/mri/2V1+aseg.mgz
It creates the 2V1+aseg.mgz file and I tried opening it in freeview with the color lookup table that I used when I made it into an annotation file and its all black. Without the color lookup table it is
all white.
Clicking around the values are 41, 0, or 2000 etc., but I can’t visually see anything. What have I done wrong here?
As I mentioned before, I just want to use these label file for diffusion tractography, so if I am heading down the wrong path, I would appreciate advice.
Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Platform: linux based cluster
Thank you!
Sara Sims