afni.nimh.nih.gov

Hi folks.
I have converted .IMG files into AFNI, and now want to scalp them. When I use 3dIntracranial, I get no image. Here is the readout from one of my files:

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[jgf@dhcppc3 Families18-35]$ 3dIntracranial -anat rot23dbM+orig -prefix Srot23dbM+orig


Program: 3dIntracranial
Author: B. D. Ward
Initial Release: 04 June 1999
Latest Revision: 02 December 2002

5795713 voxels above lower cutoff = 25

Estimating PDF of voxel intensities

Original PDF:
Number of bins = 32257
Lower bound = 256.000000
Upper bound = 32512.000000
Bin width = 1.000000

Trimmed PDF:
Number of bins = 24831
Lower bound = 257.000000
Upper bound = 25087.000000
Bin width = 1.000000

Smoothed PDF:
Number of bins = 24831
Lower bound = 257.000000
Upper bound = 25087.000000
Bin width = 1.000000

Extrema of PDF:

Num Local Min = 0

Num Local Max = 96
x[255] = 512.000 p[255] = 0.067863
x[511] = 768.000 p[511] = 0.050369
x[767] = 1024.000 p[767] = 0.035379
x[1023] = 1280.000 p[1023] = 0.024750
x[1279] = 1536.000 p[1279] = 0.018176
x[1535] = 1792.000 p[1535] = 0.013775
x[1791] = 2048.000 p[1791] = 0.010994
x[2047] = 2304.000 p[2047] = 0.009010
x[2303] = 2560.000 p[2303] = 0.007674
x[2559] = 2816.000 p[2559] = 0.006623
x[2815] = 3072.000 p[2815] = 0.005974
x[3071] = 3328.000 p[3071] = 0.005455
x[3327] = 3584.000 p[3327] = 0.004968
x[3583] = 3840.000 p[3583] = 0.004670
x[3839] = 4096.000 p[3839] = 0.004429
x[4095] = 4352.000 p[4095] = 0.004239
x[4351] = 4608.000 p[4351] = 0.004014
x[4607] = 4864.000 p[4607] = 0.003874
x[4863] = 5120.000 p[4863] = 0.003765
x[5119] = 5376.000 p[5119] = 0.003689
x[5375] = 5632.000 p[5375] = 0.003616
x[5631] = 5888.000 p[5631] = 0.003607
x[5887] = 6144.000 p[5887] = 0.003553
x[6143] = 6400.000 p[6143] = 0.003531
x[6399] = 6656.000 p[6399] = 0.003511
x[6655] = 6912.000 p[6655] = 0.003579
x[6911] = 7168.000 p[6911] = 0.003544
x[7167] = 7424.000 p[7167] = 0.003594
x[7423] = 7680.000 p[7423] = 0.003709
x[7679] = 7936.000 p[7679] = 0.003772
x[7935] = 8192.000 p[7935] = 0.003902
x[8191] = 8448.000 p[8191] = 0.004010
x[8447] = 8704.000 p[8447] = 0.004157
x[8703] = 8960.000 p[8703] = 0.004286
x[8959] = 9216.000 p[8959] = 0.004455
x[9215] = 9472.000 p[9215] = 0.004687
x[9471] = 9728.000 p[9471] = 0.004899
x[9727] = 9984.000 p[9727] = 0.005084
x[9983] = 10240.000 p[9983] = 0.005254
x[10239] = 10496.000 p[10239] = 0.005388
x[10495] = 10752.000 p[10495] = 0.005433
x[10751] = 11008.000 p[10751] = 0.005419
x[11007] = 11264.000 p[11007] = 0.005397
x[11263] = 11520.000 p[11263] = 0.005367
x[11519] = 11776.000 p[11519] = 0.005192
x[11775] = 12032.000 p[11775] = 0.005098
x[12031] = 12288.000 p[12031] = 0.004998
x[12287] = 12544.000 p[12287] = 0.004875
x[12543] = 12800.000 p[12543] = 0.004748
x[12799] = 13056.000 p[12799] = 0.004620
x[13055] = 13312.000 p[13055] = 0.004585
x[13311] = 13568.000 p[13311] = 0.004611
x[13567] = 13824.000 p[13567] = 0.004638
x[13823] = 14080.000 p[13823] = 0.004702
x[14079] = 14336.000 p[14079] = 0.004685
x[14335] = 14592.000 p[14335] = 0.004596
x[14591] = 14848.000 p[14591] = 0.004342
x[14847] = 15104.000 p[14847] = 0.003990
x[15103] = 15360.000 p[15103] = 0.003570
x[15359] = 15616.000 p[15359] = 0.003141
x[15615] = 15872.000 p[15615] = 0.002673
x[15871] = 16128.000 p[15871] = 0.002254
x[16127] = 16384.000 p[16127] = 0.001914
x[16383] = 16640.000 p[16383] = 0.001632
x[16639] = 16896.000 p[16639] = 0.001445
x[16895] = 17152.000 p[16895] = 0.001280
x[17151] = 17408.000 p[17151] = 0.001156
x[17407] = 17664.000 p[17407] = 0.001049
x[17663] = 17920.000 p[17663] = 0.000987
x[17919] = 18176.000 p[17919] = 0.000953
x[18175] = 18432.000 p[18175] = 0.000911
x[18431] = 18688.000 p[18431] = 0.000900
x[18687] = 18944.000 p[18687] = 0.000875
x[18943] = 19200.000 p[18943] = 0.000842
x[19199] = 19456.000 p[19199] = 0.000841
x[19455] = 19712.000 p[19455] = 0.000822
x[19711] = 19968.000 p[19711] = 0.000786
x[19967] = 20224.000 p[19967] = 0.000772
x[20223] = 20480.000 p[20223] = 0.000764
x[20479] = 20736.000 p[20479] = 0.000746
x[20735] = 20992.000 p[20735] = 0.000751
x[20991] = 21248.000 p[20991] = 0.000741
x[21247] = 21504.000 p[21247] = 0.000733
x[21503] = 21760.000 p[21503] = 0.000743
x[21759] = 22016.000 p[21759] = 0.000717
x[22015] = 22272.000 p[22015] = 0.000717
x[22271] = 22528.000 p[22271] = 0.000698
x[22527] = 22784.000 p[22527] = 0.000677
x[22783] = 23040.000 p[22783] = 0.000662
x[23039] = 23296.000 p[23039] = 0.000631
x[23295] = 23552.000 p[23295] = 0.000637
x[23551] = 23808.000 p[23551] = 0.000608
x[23807] = 24064.000 p[23807] = 0.000593
x[24063] = 24320.000 p[24063] = 0.000581
x[24319] = 24576.000 p[24319] = 0.000544
x[24575] = 24832.000 p[24575] = 0.000529

Initial PDF estimates:
Lower Bnd = 257.000 Upper Bnd = 25087.000
Gray Peak = 512.000 White Peak = 768.000

Probability Density Function Estimates:
Background Coef = 0.749566
Background Mean = 296.252350
Background Std Dev = 10112.095703
Gray Matter Coef = 0.121026
Gray Matter Mean = 512.083984
Gray Matter Std Dev = 2.830307
White Matter Coef = 0.231016
White Matter Mean = 793.016174
White Matter Std Dev = 118.752350

rmse = 0.001273

Control inputs:
anat filename = rot23dbM+orig
min value = 506.423370
max value = 1030.520874
min conn = 4
max conn = 2
prefix filename = Srot23dbM+orig

Calculating center of mass
Center of mass: ix = 109 jy = 113 kz = 47

Segmenting slices perpendicular to y-axis

Segmenting slices perpendicular to z-axis

Segmenting slices perpendicular to x-axis

Creating envelope for segmented image

Performing voxel connectivity tests

Writing anatomical dataset: ./Srot23dbM+orig.HEAD

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Any help would be appreciated!

Jodene
U of Texas, Austin