Re: [Freesurfer] mri_aparc2aseg bad incorrect ROIs

2022-06-21 Thread Benjamin Deck 
External Email - Use Caution

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.

https://secure-web.cisco.com/1uK1SqmLnsjHZpvlRJyITHKYUhsrOBcU7gkc7GagN0OUsbxgbuaXR7mJEmN0D9LHVvpNjZScCPthfFK0-9DMt-JMGIobJ0Nwvjv6_dhtQwajnyRV-kWYGhspgxGFAHobEFgm1BMAz6KLv1bPDs0bfsrNkxyEXnOh89JZKO57Zx_8Y28sU2xHewG4MD2qUokz-rsz_Q-LS4Sm1TweiFTdAd5rdvZ1_CIQ58pI-qz5T-dSCp-XWl7LVsG22IpD_nFN8juENy27iFWfgh-2IhA3NYK7kXMdWYfu_s5zrX-0_JlLlPfDnE6F53WSFLralPOyd/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg56796.html




Any ideas?



On Tue, Jun 21, 2022 at 1:48 PM Benjamin Deck  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-Cortex205 62  78  0
> 4   Left-Lateral-Ventricle  120 18  134 0
> 5   Left-Inf-Lat-Vent   196 58  250 0
> 6   Left-Cerebellum-Exterior0   148 0   0
> 7   Left-Cerebellum-White-Matter220 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:*
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> *mri_aparc2aseg --s sub-DAEK --annot yeo2011 --annot-table
> sub-DAEK_yeoLUT.txt --threads 6 --rip-unknown --volmask --aseg
> aseg.presurf.hyposSUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjectssubject
> sub-DAEKoutvol
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/yeo2011+aseg.mgzuseribbon
> 0baseoffset 0RipUnknown 18 avail.processors, using 6Reading lh white
> surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.whiteReading
> lh pial
> surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.pialLoading
> lh annotations from
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annotHave
> color table for lh white annotationRipping vertices labeled as unkownRipped
> 27062 vertices from left hemiBuilding hash of lh whiteBuilding hash of lh
> pialReading rh white
> surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/rh.whiteReading
> rh pial
> surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/rh.pialLoading
> rh annotations from
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/rh.yeo2011.annotHave
> color table for rh white annotationRipping vertices labeled as unkownRipped
> 27560 vertices from right hemiBuilding hash of rh whiteBuilding hash of rh
> pialLoading ribbon segmentation from
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/ribbon.mgzLoading aseg
> from
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/aseg.presurf.hypos.mgzASeg
> Vox2RAS: 0.8   0.0   0.0   127.9; 0.0
> 0.0   0.8  -127.9; 0.0  -0.8   0.0
> 127.9; 0.0   0.0   0.0
> 1.0;-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  19287  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
>  39306  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  79109 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 219114  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  99173 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 239179240 128 241 242 243 180 244
> 129 245 246 247 248 181 249 250 251 130 252 253 254 255 256 257 258 259260
> 261 262

Re: [Freesurfer] mri_aparc2aseg bad incorrect ROIs

2022-06-21 Thread Benjamin Deck 
External Email - Use Caution

 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-Cortex205 62  78  0
4   Left-Lateral-Ventricle  120 18  134 0
5   Left-Inf-Lat-Vent   196 58  250 0
6   Left-Cerebellum-Exterior0   148 0   0
7   Left-Cerebellum-White-Matter220 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.hyposSUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjectssubject
sub-DAEKoutvol
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/yeo2011+aseg.mgzuseribbon
0baseoffset 0RipUnknown 18 avail.processors, using 6Reading lh white
surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.whiteReading
lh pial
surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.pialLoading
lh annotations from
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annotHave
color table for lh white annotationRipping vertices labeled as unkownRipped
27062 vertices from left hemiBuilding hash of lh whiteBuilding hash of lh
pialReading rh white
surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/rh.whiteReading
rh pial
surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/rh.pialLoading
rh annotations from
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/rh.yeo2011.annotHave
color table for rh white annotationRipping vertices labeled as unkownRipped
27560 vertices from right hemiBuilding hash of rh whiteBuilding hash of rh
pialLoading ribbon segmentation from
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/ribbon.mgzLoading aseg
from
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/aseg.presurf.hypos.mgzASeg
Vox2RAS: 0.8   0.0   0.0   127.9; 0.0
0.0   0.8  -127.9; 0.0  -0.8   0.0
127.9; 0.0   0.0   0.0
1.0;-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  19287  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
 39306  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  79109 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 219114  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  99173 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 239179240 128 241 242 243 180 244
129 245 246 247 248 181 249 250 251 130 252 253 254 255 256 257 258 259260
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 139197 140 198 141 199142 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 159160 nctx = 1191735Used brute-force
search on 1567 voxelsWriting output aseg to
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/yeo2011+aseg.mgz#VMPC#
mri_aparc2aseg VmPeak  2534656mri_aparc2aseg done*

Re: [Freesurfer] mri_aparc2aseg bad incorrect ROIs

2022-06-19 Thread Douglas N. Greve 
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/

 
	Virus-free. *MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* www.avast.com 
 




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[Freesurfer] mri_aparc2aseg bad incorrect ROIs

2022-06-13 Thread Benjamin Deck 
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*


Virus-free.
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