Hi Doug,

Thanks for getting back to me.

Yes, it's very weird. My LUT doesn't contain any subcortical structures but when I load my custom LUT into Freeview, it shows my surface-based parcellation in the subcortical regions. Furthermore, my annotation files look completely fine!

I noticed that the indices of my LUT are the same as the default LUT, could this be a problem; should my custom LUT have unique index IDs?

For example see the two LUTs:

FS default LUT:

#No. Label Name: R G B A

0 Unknown 0 0 0 0
1 Left-Cerebral-Exterior 70 130 180 0
2 Left-Cerebral-White-Matter 245 245 245 0
3 Left-Cerebral-Cortex 205 62 78 0
4 Left-Lateral-Ventricle 120 18 134 0
5 Left-Inf-Lat-Vent 196 58 250 0
6 Left-Cerebellum-Exterior 0 148 0 0
7 Left-Cerebellum-White-Matter 220 248 164 0

.....

My Custom LUT

0 Unknown 0 0 0 0
1 Net_10_ROIs_1_lh_native 255 255 255 0
2 Net_11_ROIs_1_lh_native 25 5 25 0
3 Net_12_ROIs_1_lh_native 25 100 40 0
4 Net_12_ROIs_2_lh_native 70 130 180 0
5 Net_13_ROIs_1_lh_native 100 100 0 0
6 Net_13_ROIs_2_lh_native 196 58 250 0
7 Net_13_ROIs_3_lh_native 100 25 0 0

.....

Output from the call with your suggestion of --aseg flag:

mri_aparc2aseg --s sub-DAEK --annot yeo2011 --annot-table sub-DAEK_yeoLUT.txt --threads 6 --rip-unknown --volmask --aseg aseg.presurf.hypos
SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects
subject sub-DAEK
outvol /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/yeo2011+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 1
8 avail.processors, using 6

Reading lh white surface
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.white

Reading lh pial surface
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.pial

Loading lh annotations from /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annot
Have color table for lh white annotation
Ripping vertices labeled as unkown
Ripped 27062 vertices from left hemi

Building hash of lh white

Building hash of lh pial

Reading rh white surface
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/rh.white

Reading rh pial surface
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/rh.pial

Loading rh annotations from /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/rh.yeo2011.annot
Have color table for rh white annotation
Ripping vertices labeled as unkown
Ripped 27560 vertices from right hemi

Building hash of rh white

Building hash of rh pial
Loading ribbon segmentation from /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/ribbon.mgz

Loading aseg from /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-0.80000 0.00000 0.00000 127.99999;
0.00000 0.00000 0.80000 -127.99999;
0.00000 -0.80000 0.00000 127.99999;
0.00000 0.00000 0.00000 1.00000;
-------------------------

Labeling Slice (320)
161 108 214 54 0 267 1 55 268 2 269 56 3 270 57 4 271 58 272 5 59
6 273 60 7 274 61 275 8 62 276 9 63 277 10 64 278 11 65 279
12 66 280 67 13 281 68 14 282 15 69 283 16 284 70 17 285 18 286 19
287 20 71 288 21 289 22 290 23 291 24 292 25 293 26 294 27 295 28 72 296 29 297 30 298 31 299
32 300 33 301 34 302 35 303 36 304 37 38 305 39
306 40 307 41 308 42 309 43 310 44 311 45 73 312 46 313 47 314 48 315 49 316 50 317 51 318 52 319
53 74 75 76 77 78 79
109 162 80 215 81 82 163 110 83 216 164 84 111 85 165 86 217 112 87 166 88 218 113 89 167 90 219
114 91 168 115 92 220 169 93 116 221 94 117 170 222 95 118 96 223 171 119
97 224 172 120 225 98 226 121 99
173 227 100 122 228 174 101 123 229 102 230 175 124 103 231 176 232 125 104 233 234 105 177 126 235 236 106 178 127 237 238 107 239
179
240 128 241 242 243 180 244 129 245 246 247 248 181 249 250 251 130 252 253 254 255 256 257 258 259
260 261 262 263 264 265 266 182 183 131 184 185 186 132 187 188 133 189 190 134 191 135 192 193 136 194 137 195 138 196 139
197 140 198 141 199
142 200 201 143 202 144 203 145 204 205 146 206 147 207 148 208 149 209 150 210 151 211 152 212 153 213 154 155 156 157 158 159
160 nctx = 1191735
Used brute-force search on 1567 voxels
Writing output aseg to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/yeo2011+aseg.mgz
#VMPC# mri_aparc2aseg VmPeak 2534656
mri_aparc2aseg done

On Sun, Jun 19, 2022 at 10:47 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

I'm not sure what is happening. Does cortex have label value that are just not in the LUT or are the values 0?
Try adding --aseg aseg.presurf.hypos
If you need more help,make sure to include the full terminal output

On 6/13/2022 4:49 PM, Benjamin Deck wrote:
External Email - Use Caution

Hi Freesurfer experts,

I am attempting to turn my surface-based parcellation into a segmentation file using the following command:

mri_aparc2aseg --s sub-DAEK --annot yeo2011 --annot-table sub-DAEK_yeoLUT.txt --threads 6 --rip-unknown --volmask

However, when I load the resulting volume using my custom LUT the ROIs get labeled to the white matter and subcortical structures leaving the grey matter unlabeled.

When I examine the annotation files, they look appropriate and there isn't any overlap.

Do I need to include the subcortical structures in my custom LUT to avoid this from happening or is there a better solution?

Thank you!

--

Benjamin L. Deck
Doctoral Student

Applied Cognitive and Brain Sciences

Department of Psychological and Brain Sciences

Drexel University

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