Hello,

I'm running into the following error when I try running to3d to convert my DICOM files to NIFTI

to3d -prefix dan_test -time:zt 72 276 1000 FROM_IMAGE *_-0002*.dcm

++ to3d: AFNI version=AFNI_16.3.00 (Oct 10 2016) [64-bit]
++ Authored by: RW Cox
++ It is best to use to3d via the Dimon program.
*+ WARNING: TR expressed in milliseconds will be converted to TR=1.000000s
++ Counting images: total=276 2D slices
** Number of slices on command line = 276
** Number of slices needed for -time: = 19872
** Something is wrong with your command line!



I ran the Dimon command, and this it the output from that:

Dimon -infile_pattern '*_-0002-*.dcm' -quit

Dimon version 4.16 (July 8, 2016) running, use <ctrl-c> to quit...

-- scanning for first volume
++ Data detected to be oblique
*+ WARNING: DICOM file ADM5_1007_-0002-0001-00001.dcm:
--> unsigned 16-bit; AFNI stores as signed; 55 pixels < 0
--> consider 'to3d -ushort2float', if not already being applied
*+ WARNING: Bad DICOM header - assuming oblique scaling direction!

-- first volume found (1 slices)
-- scanning for additional volumes...
-- run 2: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 . . .

final run statistics:
volume info :
slices : 1
z_first : 299.3
z_last : 299.3
z_delta : 2
oblique : yes
mos_nslices : 0

run # 2 : volumes = 276, first file (#0) = ADM5_1007_-0002-0001-00001.dcm


I've seen a few older posts where people were having similar issues, and some have resorted to using AFNI's imcutup command (assuming I've lost the mosaic information). I was wondering if there are other options for dealing with this issue?

Thank you,

Dan