Hi Chris, 

I'm having a similar issue as Paul for T1ws and PA direction DTI images. I did check the dicom headers closely, and based on slice location/instance numbers, everything seems to be accounted for (equal slice distances of ~0.8, consistently ascending instance number (by the value of 1)). I was wondering what you might recommend? 

Here is the output for T1w: 

Warning: Interslice distance varies in this volume (incompatible with NIfTI format).

Warning: Missing images? Expected 223 images, but instance number (0020,0013) ranges from 1 to 224

Unable to equalize slice distances: slice order not consistently ascending:

dx=[0 0 0.799999 1.6 2.4 3.2 4 4.8 5.6 6.4 7.2 8 8.8 9.6 10.4 11.2 12 12.8 13.6 14.4 15.2 16 16.8 17.6 18.4 19.2 20 20.8 21.6 22.4 23.2 24 24.8 25.6 26.4 27.2 28 28.8 29.6 30.4 31.2 32 32.8 33.6 34.4 35.2 36 36.8 37.6 38.4 39.2 40 40.8 41.6 42.4 43.2 44 44.8 45.6 46.4 47.2 48 48.8 49.6 50.4 51.2 52 52.8 53.6 54.4 55.2 56 56.8 57.6 58.4 59.2 60 60.8 61.6 62.4 63.2 64 64.8 65.6 66.4 67.2 68 68.8 69.6 70.4 71.2 72 72.8 73.6 74.4 75.2 76 76.8 77.6 78.4 79.2 80 80.8 81.6 82.4 83.2 84 84.8 85.6 86.4 87.2 88 88.8 89.6 90.4 91.2 92 92.8 93.6 94.4 95.2 96 96.8 97.6 98.4 99.2 100 100.8 101.6 102.4 103.2 104 104.8 105.6 106.4 107.2 108.8 109.6 110.4 111.2 112 112.8 113.6 114.4 115.2 116 116.8 117.6 118.4 119.2 120 120.8 121.6 122.4 123.2 124 124.8 125.6 126.4 127.2 128 128.8 129.6 130.4 131.2 132 132.8 133.6 134.4 135.2 136 136.8 137.6 138.4 139.2 140 140.8 141.6 142.4 143.2 144 144.8 145.6 146.4 147.2 148 148.8 149.6 150.4 151.2 152 152.8 153.6 154.4 155.2 156 156.8 157.6 158.4 159.2 160 160.8 161.6 162.4 163.2 164 164.8 165.6 166.4 167.2 168 168.8 169.6 170.4 171.2 172 172.8 173.6 174.4 175.2 176 176.8 177.6 178.4 3.07165e-41 -1.60121e+13 3.07165e-41 2.34087e-41 0 -2.21374e-24 4.57005e-41 -2.21374e-24 4.57005e-41 0 0 0 0 0 3.60608e-06 2.04793e-38 3.52657e-38 9.18369e-41 9.18369e-41 0 0 0 3.67342e-40 2.24208e-44 1 0.8 0.8 0.8 2.4 0 0 0 352 1 0 6.16298e-33 0 0 0 0 0 0 1.1017e-08 3.21607e+12 0.0560125 2.64037e-06 6.33736e-10 2.31766e+29 7.18332e+22 1.76634e-41 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9.18369e-41 0.0645953 0.0228613 -0.0161774 -95.6073 -91.4316 -169.645 0.798744 0.0281824 0.0348153 -95.6073 -0.0234568 0.792905 -0.103688 -91.4316 -0.0381592 0.102504 0.792488 -169.645 0 0 0 0 4.51552e-39 0 1.26274e-38 0 2.2893e-41]

Recompiling with '-DmyInstanceNumberOrderIsNotSpatial' might help.

And DTI-PA: 

Warning: Interslice distance varies in this volume (incompatible with NIfTI format).

Warning: Missing images? Expected 89 images, but instance number (0020,0013) ranges from 1 to 90

Only able to make equidistant slices from 8,16,24-bit integer or 32-bit float image data.

Any insight is appreciated, thank you!