AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

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June 24, 2022 05:02AM
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 -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
Subject Author Posted

Question about 3dSkullStrip

Sue_TS June 21, 2022 04:42AM

Re: Question about 3dSkullStrip

rick reynolds June 22, 2022 02:09PM

Re: Question about 3dSkullStrip

Sue_TS June 24, 2022 05:02AM