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Hi Doug,

I think I may have found a similar issue via the mailing list which I hadn't noticed before. However, it's not clear to me how to implement this solution.

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Any ideas?



On Tue, Jun 21, 2022 at 1:48 PM Benjamin Deck <bdeck8317@gmail.com> wrote:
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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--
Benjamin L. Deck
Doctoral Student
Applied Cognitive and Brain Sciences
Department of Psychological and Brain Sciences
Drexel University


--
Benjamin L. Deck
Doctoral Student
Applied Cognitive and Brain Sciences
Department of Psychological and Brain Sciences
Drexel University