Question about 3dSkullStrip

AFNI Message Board
1

Hi experts,

I was using 3dSkullStrip to remove skull of mice images by following command:
"3dSkullStrip -prefix mask -orig_vol -input base+orig"
where "base+orig" came from "3dTstat -prefix base -mean function.nii".

And I got error message like this:
"--     Error SUMA_LoadPrepInVol (SUMA_BrainWrap.c:77):
 98 percentile is 0!
 What kind of dataset is this?
 --     Error 3dSkullStrip (SUMA_3dSkullStrip.c:2131):
 Failed to load/prep volume"

Does anyone could help me about this? Many thanks in advance!!

Best regards,
Tianshu

2

Hi Tianshu,

Can you indeed verify what is in that dataset? If it shows the 98 %-ile as zero, it seems problematic.

What does this show?

3dBrickStat -perc_quiet -percentile 0 1 100 base+orig
  • rick
3

Hi rick,

The output of this command is like this:
"tianshu@ubuntu:~/Desktop/1/dicom$ 3dinfo mean+orig.
++ 3dinfo: AFNI version=AFNI_22.1.13 (Jun  6 2022) [64-bit]

Dataset File:    mean+orig
Identifier Code: AFN_egxtYprYQt_yRXf_CDX5Bg  Creation Date: Tue Jun 21 01:05:18 2022
Template Space:  ORIG
Dataset Type:    Func-Bucket (-fbuc)
Byte Order:      LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode:    BRIK
Storage Space:   1,960,000 (2.0 million) bytes
Geometry String: "MATRIX(0.3,0,0,-15,0,-0.3,0,7.18492,0,0,0.400001,-12.60653):100,70,70"
Data Axes Tilt:  Plumb
Data Axes Orientation:
  first  (x) = Right-to-Left
  second (y) = Posterior-to-Anterior
  third  (z) = Inferior-to-Superior   [-orient RPI]
R-to-L extent:   -15.000 [R] -to-    14.700 [L] -step-     0.300 mm [100 voxels]
A-to-P extent:   -13.515 [A] -to-     7.185 [P] -step-     0.300 mm [ 70 voxels]
I-to-S extent:   -12.607 [I] -to-    14.994 [S] -step-     0.400 mm [ 70 voxels]
Number of values stored at each pixel = 1
  -- At sub-brick #0 'Mean' datum type is float:      5442.12 to        546270

----- HISTORY -----
[tianshu@ubuntu: Tue Jun 21 01:05:19 2022] {AFNI_22.1.13:linux_ubuntu_16_64} 3dTstat -prefix mean -mean function.nii

tianshu@ubuntu:~/Desktop/1/dicom$ 3dBrickStat -perc_quiet -percentile 0 1 100 mean+orig
5442.125488   6263.021484   6457.299316   6646.797852   6911.141113   7153.189941   7424.698730   7692.226074   7981.251953   8276.647461       
8568.061523   8870.624023   9176.370117   9486.892578   9791.843750   10093.606445   10392.186523   10670.067383   10940.783203   11181.240234   
11396.216797   11575.361328   11720.275391   11850.057617   11967.104492   12092.906250   12220.299805   12359.631836   12511.710938   
12681.305664   12877.970703   13086.580078   13318.277344   13566.698242   13830.244141   14111.308594   14407.499023   14722.001953   
15046.857422   15380.476562   15736.381836   16106.617188   16478.451172   16865.410156   17277.054688   17698.255859   18135.375000   
18583.650391   19047.833984   19532.734375   20057.441406   20590.896484   21155.406250   21736.646484   22335.400391   22974.759766   
23636.421875   24349.027344   25083.136719   25866.609375   26715.380859   27618.283203   28555.433594   29556.267578   30679.730469   
31858.121094   33183.015625   34648.867188   36203.871094   37887.875000   39767.730469   41825.132812   44057.722656   46405.761719   
48924.984375   51521.429688   54350.398438   57299.566406   60523.429688   63962.289062   67537.273438   71299.398438   75088.546875   
78956.578125   82885.937500   87032.617188   91334.546875   96028.218750   101069.835938   106566.117188   112737.585938   119670.218750   
127582.953125   136568.281250   146865.703125   158694.312500   172516.625000   189398.718750   209575.546875   238351.500000   
546269.937500"

It seems that the value in the dataset is not empty (though it is much bigger than datasets I processed before), I am not sure if it is the reason of skullstrip error.

Tianshu