Hello AFNI,
I encountered some strange behavior involving sub-brick selection and the program 3dExtrema. The data file I am analyzing has 7 sub-bricks. The conventional way to select said sub-bricks via AFNI commands is by using file_name.nii'[n]', where n would range from 0-6 (since that is where AFNI begins counting at 0). However, here are some examples from 3dExtrema that have me scratching my head:
3dExtrema -volume -sep_dist 20 AMYG-LME-001-cluster.nii
++ 3dExtrema: AFNI version=AFNI_16.0.10 (Feb 25 2016) [64-bit]
++ Authored by: B. Douglas Ward
Reading input dataset: AMYG-LME-001-cluster.nii
Reading input dataset: AMYG-LME-001-cluster.nii
Reading volume #0
Reading volume #1
Reading volume #2
Reading volume #3
Reading volume #4
Reading volume #5
Reading volume #6
Number of volumes = 7
Maxima for Volume #0 (Coordinates Order = RAI):
Index Intensity RL[mm] AP[mm] IS[mm] Count Dist[mm]
----- --------- ------ ------ ------ ----- --------
1 1.650 15.00 3.00 -17.00 5 21.541
2 1.102 3.00 11.00 -1.00 3 21.541
3 0.875 39.00 15.00 -29.00 2 29.394
4 0.770 15.00 -13.00 -1.00 1 22.627
Maxima for Volume #1 (Coordinates Order = RAI):
Maxima for Volume #2 (Coordinates Order = RAI):
Maxima for Volume #3 (Coordinates Order = RAI):
Index Intensity RL[mm] AP[mm] IS[mm] Count Dist[mm]
----- --------- ------ ------ ------ ----- --------
1 252.880 3.00 7.00 43.00 4 48.826
2 247.490 -41.00 23.00 23.00 2 21.541
3 228.340 -29.00 15.00 7.00 3 21.541
Maxima for Volume #4 (Coordinates Order = RAI):
Index Intensity RL[mm] AP[mm] IS[mm] Count Dist[mm]
----- --------- ------ ------ ------ ----- --------
1 0.025 43.00 35.00 55.00 4
Maxima for Volume #5 (Coordinates Order = RAI):
Maxima for Volume #6 (Coordinates Order = RAI):
Index Intensity RL[mm] AP[mm] IS[mm] Count Dist[mm]
----- --------- ------ ------ ------ ----- --------
1 0.576 23.00 -1.00 -13.00 2 25.923
2 0.418 -17.00 3.00 -9.00 5 22.978
3 0.295 19.00 -17.00 -33.00 3 25.923
4 0.278 7.00 -25.00 -1.00 3 31.241
5 0.224 -25.00 -25.00 -29.00 2 25.612
6 0.204 -1.00 -41.00 27.00 2 33.226
7 0.185 -49.00 -1.00 -13.00 1 20.000
8 0.171 -33.00 79.00 23.00 5 26.833
9 0.168 -1.00 11.00 11.00 2 21.909
10 0.168 -33.00 67.00 47.00 1 26.833
11 0.145 23.00 87.00 15.00 3 20.785
12 0.141 19.00 83.00 35.00 3 20.785
13 0.138 19.00 27.00 -1.00 1 28.284
14 0.134 3.00 3.00 31.00 2 21.909
15 0.123 -9.00 91.00 11.00 2 29.394
16 0.120 -21.00 -13.00 55.00 3 24.331
17 0.114 -1.00 47.00 35.00 2 39.598
18 0.111 -37.00 51.00 11.00 3 30.725
19 0.109 3.00 -17.00 55.00 2 24.331
20 0.100 -33.00 -1.00 -25.00 1 20.000
21 0.088 -25.00 71.00 -17.00 1 36.442
22 0.062 -25.00 -25.00 7.00 1 32.985
23 -0.098 51.00 -5.00 11.00 1 37.094
Everything looks good when I run the command and do not specify a sub-brick. However, when I specifically target 0 and 1, I get the same exact output, which is obviously incorrect and not consistent with the above, or the data as I know it:
awdpt800wg3:UNC_AAL_GROWTH salzwedelap$
3dExtrema -volume -sep_dist 20 AMYG-LME-001-cluster.nii'[0]'
++ 3dExtrema: AFNI version=AFNI_16.0.10 (Feb 25 2016) [64-bit]
++ Authored by: B. Douglas Ward
Reading input dataset: AMYG-LME-001-cluster.nii[0]
Reading input dataset: AMYG-LME-001-cluster.nii[0]
Reading volume #0
Number of volumes = 1
Maxima for Volume #0 (Coordinates Order = RAI):
Index Intensity RL[mm] AP[mm] IS[mm] Count Dist[mm]
----- --------- ------ ------ ------ ----- --------
1 1.650 15.00 3.00 -17.00 5 21.541
2 1.102 3.00 11.00 -1.00 3 21.541
3 0.875 39.00 15.00 -29.00 2 29.394
4 0.770 15.00 -13.00 -1.00 1 22.627
awdpt800wg3:UNC_AAL_GROWTH salzwedelap$
3dExtrema -volume -sep_dist 20 AMYG-LME-001-cluster.nii'[1]'
++ 3dExtrema: AFNI version=AFNI_16.0.10 (Feb 25 2016) [64-bit]
++ Authored by: B. Douglas Ward
Reading input dataset: AMYG-LME-001-cluster.nii[1]
Reading input dataset: AMYG-LME-001-cluster.nii[1]
Reading volume #0
Number of volumes = 1
Maxima for Volume #0 (Coordinates Order = RAI):
Index Intensity RL[mm] AP[mm] IS[mm] Count Dist[mm]
----- --------- ------ ------ ------ ----- --------
1 1.650 15.00 3.00 -17.00 5 21.541
2 1.102 3.00 11.00 -1.00 3 21.541
3 0.875 39.00 15.00 -29.00 2 29.394
4 0.770 15.00 -13.00 -1.00 1 22.627
To make matters more confusing I have to use sub-brick selection = 7 to get the final volume...
awdpt800wg3:UNC_AAL_GROWTH salzwedelap$
3dExtrema -volume -sep_dist 20 AMYG-LME-001-cluster.nii'[7]'
++ 3dExtrema: AFNI version=AFNI_16.0.10 (Feb 25 2016) [64-bit]
++ Authored by: B. Douglas Ward
Reading input dataset: AMYG-LME-001-cluster.nii[7]
Reading input dataset: AMYG-LME-001-cluster.nii[7]
Reading volume #0
Number of volumes = 1
Maxima for Volume #0 (Coordinates Order = RAI):
Index Intensity RL[mm] AP[mm] IS[mm] Count Dist[mm]
----- --------- ------ ------ ------ ----- --------
1 0.576 23.00 -1.00 -13.00 2 25.923
2 0.418 -17.00 3.00 -9.00 5 22.978
3 0.295 19.00 -17.00 -33.00 3 25.923
4 0.278 7.00 -25.00 -1.00 3 31.241
5 0.224 -25.00 -25.00 -29.00 2 25.612
6 0.204 -1.00 -41.00 27.00 2 33.226
7 0.185 -49.00 -1.00 -13.00 1 20.000
8 0.171 -33.00 79.00 23.00 5 26.833
9 0.168 -1.00 11.00 11.00 2 21.909
10 0.168 -33.00 67.00 47.00 1 26.833
11 0.145 23.00 87.00 15.00 3 20.785
12 0.141 19.00 83.00 35.00 3 20.785
13 0.138 19.00 27.00 -1.00 1 28.284
14 0.134 3.00 3.00 31.00 2 21.909
15 0.123 -9.00 91.00 11.00 2 29.394
16 0.120 -21.00 -13.00 55.00 3 24.331
17 0.114 -1.00 47.00 35.00 2 39.598
18 0.111 -37.00 51.00 11.00 3 30.725
19 0.109 3.00 -17.00 55.00 2 24.331
20 0.100 -33.00 -1.00 -25.00 1 20.000
21 0.088 -25.00 71.00 -17.00 1 36.442
22 0.062 -25.00 -25.00 7.00 1 32.985
23 -0.098 51.00 -5.00 11.00 1 37.094
AFNI-wan-kenobi you are my only hope, please help.
-Andy
