Regularization issue

HI Slice Community,

I have been struggling for certain amount of time regarding what I have understand to be regularization.

I have a MRI of different areas encapsulated in one acquisition.
I just would like to have “blank” slices in the coordinate where there is no acquisition. With regularization activated, there is no distorsion but Slicer make weird stuff between the areas.

I Watch the image information and there were issues with th order. For example n°5 slice beiing in fact n°4 when regarding the coordinate. I changed all names but didn’t make any difference. I guess slice already made the correction.

You will find informations below.

Thanks very much for your help

JR

image

M0001 ImagePositionPatient [3] -150.300, -100.000, 21.000
M0002 ImagePositionPatient [3] -150.300, -100.000, 18.500
0003- ImagePositionPatient [3] -150.300, -100.000, 16.000
M0004 ImagePositionPatient [3] -150.300, -100.000, 13.500
0005- ImagePositionPatient [3] -150.300, -100.000, 11.000
0006- ImagePositionPatient [3] -150.300, -100.000, 8.500
0007- ImagePositionPatient [3] -150.300, -100.000, 6.000
0008- ImagePositionPatient [3] -150.300, -100.000, 3.500
M0009 ImagePositionPatient [3] -150.300, -100.000, 1.000
M0010 ImagePositionPatient [3] -150.300, -100.000, -1.500
M0011 ImagePositionPatient [3] -150.300, -100.000, -4.000
M0012 ImagePositionPatient [3] -150.300, -100.000, -6.500
0013- ImagePositionPatient [3] -150.300, -100.000, -9.000
0014- ImagePositionPatient [3] -150.300, -100.000, -11.500
0015- ImagePositionPatient [3] -150.300, -100.000, -14.000
M0016 ImagePositionPatient [3] -150.300, -100.000, -16.500
M0017 ImagePositionPatient [3] -150.300, -100.000, -19.000
M0018 ImagePositionPatient [3] -150.300, -100.000, -21.500
M0019 ImagePositionPatient [3] -150.300, -100.000, -24.000
M0020 ImagePositionPatient [3] -150.300, -100.000, -26.500
M0021 ImagePositionPatient [3] -150.300, -100.000, -29.000
M0022 ImagePositionPatient [3] -150.300, -100.000, -31.500
0023- ImagePositionPatient [3] -150.300, -100.000, -34.000
0024- ImagePositionPatient [3] -150.300, -100.000, -36.500
M0025 ImagePositionPatient [3] -150.300, -100.000, -39.000
M0026 ImagePositionPatient [3] -150.300, -100.000, -41.500
M0027 ImagePositionPatient [3] -150.300, -100.000, -44.000
M0028 ImagePositionPatient [3] -150.300, -100.000, -46.500
M0029 ImagePositionPatient [3] -150.300, -100.000, -49.000
M0030 ImagePositionPatient [3] -150.300, -100.000, -51.500
M0031 ImagePositionPatient [3] -150.300, -100.000, -54.000
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0033- ImagePositionPatient [3] -150.300, -100.000, -59.000
0034- ImagePositionPatient [3] -150.300, -100.000, -61.500
0035- ImagePositionPatient [3] -150.300, -100.000, -64.000
M0036 ImagePositionPatient [3] -150.300, -100.000, -66.500
M0037 ImagePositionPatient [3] -150.300, -100.000, -69.000
M0038 ImagePositionPatient [3] -150.300, -100.000, -71.500
M0039 ImagePositionPatient [3] -150.300, -100.000, -74.000
M0040 ImagePositionPatient [3] -150.300, -100.000, -76.500
M0041 ImagePositionPatient [3] -150.300, -100.000, -79.000
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0043- ImagePositionPatient [3] -150.300, -100.000, -84.000
0044- ImagePositionPatient [3] -150.300, -100.000, -86.500
M0045 ImagePositionPatient [3] -150.300, -100.000, -89.000
M0046 ImagePositionPatient [3] -150.300, -100.000, -91.500
M0047 ImagePositionPatient [3] -150.300, -100.000, -383.250
M0048 ImagePositionPatient [3] -150.300, -100.000, -383.875
M0049 ImagePositionPatient [3] -150.300, -100.000, -384.500
M0050 ImagePositionPatient [3] -150.300, -100.000, -385.125
M0051 ImagePositionPatient [3] -150.300, -100.000, -385.750
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0054- ImagePositionPatient [3] -150.300, -100.000, -387.625
M0055 ImagePositionPatient [3] -150.300, -100.000, -388.250
M0056 ImagePositionPatient [3] -150.300, -100.000, -388.875
M0057 ImagePositionPatient [3] -150.300, -100.000, -389.500
M0058 ImagePositionPatient [3] -150.300, -100.000, -390.125
M0059 ImagePositionPatient [3] -150.300, -100.000, -390.750
M0060 ImagePositionPatient [3] -150.300, -100.000, -391.375
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M0063 ImagePositionPatient [3] -150.300, -100.000, -393.250
M0064 ImagePositionPatient [3] -150.300, -100.000, -393.875
M0065 ImagePositionPatient [3] -150.300, -100.000, -394.500
M0066 ImagePositionPatient [3] -150.300, -100.000, -395.125
M0067 ImagePositionPatient [3] -150.300, -100.000, -395.750
M0068 ImagePositionPatient [3] -150.300, -100.000, -396.375
M0069 ImagePositionPatient [3] -150.300, -100.000, -397.000
M0070 ImagePositionPatient [3] -150.300, -100.000, -397.625
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M0072 ImagePositionPatient [3] -150.300, -100.000, -398.875
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M0074 ImagePositionPatient [3] -150.300, -100.000, -400.125
M0075 ImagePositionPatient [3] -150.300, -100.000, -400.750
M0076 ImagePositionPatient [3] -150.300, -100.000, -401.375
M0077 ImagePositionPatient [3] -150.300, -100.000, -402.000
M0078 ImagePositionPatient [3] -150.300, -100.000, -402.625
M0079 ImagePositionPatient [3] -150.300, -100.000, -403.250
M0080 ImagePositionPatient [3] -150.300, -100.000, -403.875
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M0086 ImagePositionPatient [3] -150.300, -100.000, -407.625
M0087 ImagePositionPatient [3] -150.300, -100.000, -408.250
M0088 ImagePositionPatient [3] -150.300, -100.000, -408.875
M0089 ImagePositionPatient [3] -150.300, -100.000, -409.500
M0090 ImagePositionPatient [3] -150.300, -100.000, -410.125
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M0096 ImagePositionPatient [3] -150.300, -100.000, -413.875
M0097 ImagePositionPatient [3] -150.300, -100.000, -414.500
M0098 ImagePositionPatient [3] -150.300, -100.000, -415.125
M0099 ImagePositionPatient [3] -150.300, -100.000, -415.750
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M0102 ImagePositionPatient [3] -150.300, -100.000, -417.625
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M0104 ImagePositionPatient [3] -150.300, -100.000, -418.875
M0105 ImagePositionPatient [3] -150.300, -100.000, -419.500
M0106 ImagePositionPatient [3] -150.300, -100.000, -420.125
M0107 ImagePositionPatient [3] -150.300, -100.000, -420.750
M0108 ImagePositionPatient [3] -150.300, -100.000, -421.375
M0109 ImagePositionPatient [3] -150.300, -100.000, -422.000
0110- ImagePositionPatient [3] -150.300, -100.000, -422.625
0111- ImagePositionPatient [3] -150.300, -100.000, -423.250
M0112 ImagePositionPatient [3] -150.300, -100.000, -423.875
0113- ImagePositionPatient [3] -150.300, -100.000, -424.500
0114- ImagePositionPatient [3] -150.300, -100.000, -425.125
M0115 ImagePositionPatient [3] -150.300, -100.000, -425.750
M0116 ImagePositionPatient [3] -150.300, -100.000, -426.375
M0117 ImagePositionPatient [3] -150.300, -100.000, -427.000
M0118 ImagePositionPatient [3] -150.300, -100.000, -427.625
M0119 ImagePositionPatient [3] -150.300, -100.000, -428.250
0120- ImagePositionPatient [3] -150.300, -100.000, -428.875
0121- ImagePositionPatient [3] -150.300, -100.000, -429.500
M0122 ImagePositionPatient [3] -150.300, -100.000, -430.125
0123- ImagePositionPatient [3] -150.300, -100.000, -430.750
M0124 ImagePositionPatient [3] -150.300, -100.000, -431.375
0125- ImagePositionPatient [3] -150.300, -100.000, -432.000
M0126 ImagePositionPatient [3] -150.300, -100.000, -432.625
M0127 ImagePositionPatient [3] -150.300, -100.000, -433.250
M0128 ImagePositionPatient [3] -150.300, -100.000, -433.875
M0129 ImagePositionPatient [3] -150.300, -100.000, -434.500
0130- ImagePositionPatient [3] -150.300, -100.000, -435.125
0131- ImagePositionPatient [3] -150.300, -100.000, -435.750
0132- ImagePositionPatient [3] -150.300, -100.000, -436.375
0133- ImagePositionPatient [3] -150.300, -100.000, -437.000
0134- ImagePositionPatient [3] -150.300, -100.000, -437.625
M0135 ImagePositionPatient [3] -150.300, -100.000, -438.250
M0136 ImagePositionPatient [3] -150.300, -100.000, -438.875
M0137 ImagePositionPatient [3] -150.300, -100.000, -439.500
M0138 ImagePositionPatient [3] -150.300, -100.000, -440.125
M0139 ImagePositionPatient [3] -150.300, -100.000, -440.750
0140- ImagePositionPatient [3] -150.300, -100.000, -441.375
0141- ImagePositionPatient [3] -150.300, -100.000, -442.000
M0142 ImagePositionPatient [3] -150.300, -100.000, -442.625
M0143 ImagePositionPatient [3] -150.300, -100.000, -443.250
M0144 ImagePositionPatient [3] -150.300, -100.000, -443.875
M0145 ImagePositionPatient [3] -150.300, -100.000, -444.500
M0146 ImagePositionPatient [3] -150.300, -100.000, -445.125
M0147 ImagePositionPatient [3] -150.300, -100.000, -445.750
M0148 ImagePositionPatient [3] -150.300, -100.000, -446.375
M0149 ImagePositionPatient [3] -150.300, -100.000, -447.000
0150- ImagePositionPatient [3] -150.300, -100.000, -447.625
0151- ImagePositionPatient [3] -150.300, -100.000, -448.250
0152- ImagePositionPatient [3] -150.300, -100.000, -448.875
0153- ImagePositionPatient [3] -150.300, -100.000, -449.500
0154- ImagePositionPatient [3] -150.300, -100.000, -450.125
0155- ImagePositionPatient [3] -150.300, -100.000, -450.750
M0156 ImagePositionPatient [3] -150.300, -100.000, -451.375
M0157 ImagePositionPatient [3] -150.300, -100.000, -452.000
M0158 ImagePositionPatient [3] -150.300, -100.000, -452.625
M0159 ImagePositionPatient [3] -150.300, -100.000, -453.250
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0161- ImagePositionPatient [3] -150.300, -100.000, -454.500
0162- ImagePositionPatient [3] -150.300, -100.000, -455.125
M0163 ImagePositionPatient [3] -150.300, -100.000, -455.750
M0164 ImagePositionPatient [3] -150.300, -100.000, -456.375
M0165 ImagePositionPatient [3] -150.300, -100.000, -457.000
M0166 ImagePositionPatient [3] -150.300, -100.000, -457.625
M0167 ImagePositionPatient [3] -150.300, -100.000, -458.250
M0168 ImagePositionPatient [3] -150.300, -100.000, -458.875
M0169 ImagePositionPatient [3] -150.300, -100.000, -459.500
M0170 ImagePositionPatient [3] -150.300, -100.000, -460.125
M0171 ImagePositionPatient [3] -150.300, -100.000, -460.750
M0172 ImagePositionPatient [3] -150.300, -100.000, -461.375
M0173 ImagePositionPatient [3] -150.300, -100.000, -462.000
M0174 ImagePositionPatient [3] -150.300, -100.000, -462.625
M0175 ImagePositionPatient [3] -150.300, -100.000, -463.250
M0176 ImagePositionPatient [3] -150.300, -100.000, -463.875
M0177 ImagePositionPatient [3] -150.300, -100.000, -464.500
M0178 ImagePositionPatient [3] -150.300, -100.000, -465.125
M0179 ImagePositionPatient [3] -150.300, -100.000, -465.750
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0181- ImagePositionPatient [3] -150.300, -100.000, -467.000
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0183- ImagePositionPatient [3] -150.300, -100.000, -468.250
0184- ImagePositionPatient [3] -150.300, -100.000, -468.875
M0185 ImagePositionPatient [3] -150.300, -100.000, -469.500
M0186 ImagePositionPatient [3] -150.300, -100.000, -470.125
M0187 ImagePositionPatient [3] -150.300, -100.000, -470.750
M0188 ImagePositionPatient [3] -150.300, -100.000, -471.375
M0189 ImagePositionPatient [3] -150.300, -100.000, -472.000
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M0191 ImagePositionPatient [3] -150.300, -100.000, -473.250
0192- ImagePositionPatient [3] -150.300, -100.000, -473.875
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M0196 ImagePositionPatient [3] -150.300, -100.000, -476.375
M0197 ImagePositionPatient [3] -150.300, -100.000, -477.000
M0198 ImagePositionPatient [3] -150.300, -100.000, -477.625
M0199 ImagePositionPatient [3] -150.300, -100.000, -478.250
0200- ImagePositionPatient [3] -150.300, -100.000, -478.875
0201- ImagePositionPatient [3] -150.300, -100.000, -479.500
0202- ImagePositionPatient [3] -150.300, -100.000, -480.125
M0203 ImagePositionPatient [3] -150.300, -100.000, -480.750
0204- ImagePositionPatient [3] -150.300, -100.000, -481.375
0205- ImagePositionPatient [3] -150.300, -100.000, -482.000
M0206 ImagePositionPatient [3] -150.300, -100.000, -482.625
M0207 ImagePositionPatient [3] -150.300, -100.000, -483.250
M0208 ImagePositionPatient [3] -150.300, -100.000, -483.875
M0209 ImagePositionPatient [3] -150.300, -100.000, -484.500
0210- ImagePositionPatient [3] -150.300, -100.000, -485.125
0211- ImagePositionPatient [3] -150.300, -100.000, -485.750
0212- ImagePositionPatient [3] -150.300, -100.000, -486.375
M0213 ImagePositionPatient [3] -150.300, -100.000, -487.000
0214- ImagePositionPatient [3] -150.300, -100.000, -487.625
0215- ImagePositionPatient [3] -150.300, -100.000, -488.250
M0216 ImagePositionPatient [3] -150.300, -100.000, -488.875
M0217 ImagePositionPatient [3] -150.300, -100.000, -489.500
M0218 ImagePositionPatient [3] -150.300, -100.000, -490.125
M0219 ImagePositionPatient [3] -150.300, -100.000, -490.750
0220- ImagePositionPatient [3] -150.300, -100.000, -491.375
0221- ImagePositionPatient [3] -150.300, -100.000, -492.000
0222- ImagePositionPatient [3] -150.300, -100.000, -492.625
0223- ImagePositionPatient [3] -150.300, -100.000, -493.250
M0224 ImagePositionPatient [3] -150.300, -100.000, -493.875
M0225 ImagePositionPatient [3] -150.300, -100.000, -494.500
M0226 ImagePositionPatient [3] -150.300, -100.000, -495.125
M0227 ImagePositionPatient [3] -150.300, -100.000, -495.750
M0228 ImagePositionPatient [3] -150.300, -100.000, -496.375
M0229 ImagePositionPatient [3] -150.300, -100.000, -497.000
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0233- ImagePositionPatient [3] -150.300, -100.000, -499.500
0234- ImagePositionPatient [3] -150.300, -100.000, -500.125
0235- ImagePositionPatient [3] -150.300, -100.000, -500.750
M0236 ImagePositionPatient [3] -150.300, -100.000, -501.375
M0237 ImagePositionPatient [3] -150.300, -100.000, -502.000
M0238 ImagePositionPatient [3] -150.300, -100.000, -502.625
M0239 ImagePositionPatient [3] -150.300, -100.000, -503.250
M0240 ImagePositionPatient [3] -150.300, -100.000, -505.750
M0241 ImagePositionPatient [3] -150.300, -100.000, -507.000
M0242 ImagePositionPatient [3] -150.300, -100.000, -503.875
M0243 ImagePositionPatient [3] -150.300, -100.000, -504.500
M0244 ImagePositionPatient [3] -150.300, -100.000, -505.125
M0245 ImagePositionPatient [3] -150.300, -100.000, -506.375
M0246 ImagePositionPatient [3] -150.300, -100.000, -507.625
M0247 ImagePositionPatient [3] -150.300, -100.000, -508.250
M0248 ImagePositionPatient [3] -150.300, -100.000, -508.875
M0249 ImagePositionPatient [3] -150.300, -100.000, -509.500
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0251- ImagePositionPatient [3] -150.300, -100.000, -510.750
0252- ImagePositionPatient [3] -150.300, -100.000, -511.375
0253- ImagePositionPatient [3] -150.300, -100.000, -512.000
0254- ImagePositionPatient [3] -150.300, -100.000, -512.625
0255- ImagePositionPatient [3] -150.300, -100.000, -513.250
M0256 ImagePositionPatient [3] -150.300, -100.000, -513.875
M0257 ImagePositionPatient [3] -150.300, -100.000, -514.500
M0258 ImagePositionPatient [3] -150.300, -100.000, -515.125
M0259 ImagePositionPatient [3] -150.300, -100.000, -515.750
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0263- ImagePositionPatient [3] -150.300, -100.000, -518.250
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M0266 ImagePositionPatient [3] -150.300, -100.000, -520.125
M0267 ImagePositionPatient [3] -150.300, -100.000, -520.750
M0268 ImagePositionPatient [3] -150.300, -100.000, -521.375
M0269 ImagePositionPatient [3] -150.300, -100.000, -522.000
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0274- ImagePositionPatient [3] -150.300, -100.000, -525.125
0275- ImagePositionPatient [3] -150.300, -100.000, -525.750
M0276 ImagePositionPatient [3] -150.300, -100.000, -526.375
M0277 ImagePositionPatient [3] -150.300, -100.000, -527.000
M0278 ImagePositionPatient [3] -150.300, -100.000, -527.625
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0283- ImagePositionPatient [3] -150.300, -100.000, -530.750
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M0288 ImagePositionPatient [3] -150.300, -100.000, -533.875
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M0290 ImagePositionPatient [3] -150.300, -100.000, -535.125
M0291 ImagePositionPatient [3] -150.300, -100.000, -535.750
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M0293 ImagePositionPatient [3] -150.300, -100.000, -537.000
M0294 ImagePositionPatient [3] -150.300, -100.000, -537.625
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M0297 ImagePositionPatient [3] -150.300, -100.000, -795.000
M0298 ImagePositionPatient [3] -150.300, -100.000, -797.500
M0299 ImagePositionPatient [3] -150.300, -100.000, -800.000
M0300 ImagePositionPatient [3] -150.300, -100.000, -802.500
M0301 ImagePositionPatient [3] -150.300, -100.000, -805.000
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0303- ImagePositionPatient [3] -150.300, -100.000, -810.000
0304- ImagePositionPatient [3] -150.300, -100.000, -812.500
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M0306 ImagePositionPatient [3] -150.300, -100.000, -817.500
M0307 ImagePositionPatient [3] -150.300, -100.000, -820.000
M0308 ImagePositionPatient [3] -150.300, -100.000, -822.500
M0309 ImagePositionPatient [3] -150.300, -100.000, -825.000
M0310 ImagePositionPatient [3] -150.300, -100.000, -827.500
M0311 ImagePositionPatient [3] -150.300, -100.000, -830.000
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0313- ImagePositionPatient [3] -150.300, -100.000, -835.000
M0314 ImagePositionPatient [3] -150.300, -100.000, -837.500
M0315 ImagePositionPatient [3] -150.300, -100.000, -840.000
M0316 ImagePositionPatient [3] -150.300, -100.000, -842.500
M0317 ImagePositionPatient [3] -150.300, -100.000, -845.000
M0318 ImagePositionPatient [3] -150.300, -100.000, -847.500
M0319 ImagePositionPatient [3] -150.300, -100.000, -850.000
M0320 ImagePositionPatient [3] -150.300, -100.000, -852.500
M0321 ImagePositionPatient [3] -150.300, -100.000, -855.000
M0322 ImagePositionPatient [3] -150.300, -100.000, -857.500
M0323 ImagePositionPatient [3] -150.300, -100.000, -860.000
0324- ImagePositionPatient [3] -150.300, -100.000, -862.500
0325- ImagePositionPatient [3] -150.300, -100.000, -865.000
M0326 ImagePositionPatient [3] -150.300, -100.000, -867.500
M0327 ImagePositionPatient [3] -150.300, -100.000, -870.000
M0328 ImagePositionPatient [3] -150.300, -100.000, -872.500
M0329 ImagePositionPatient [3] -150.300, -100.000, -875.000
0330- ImagePositionPatient [3] -150.300, -100.000, -877.500
0331- ImagePositionPatient [3] -150.300, -100.000, -880.000
M0332 ImagePositionPatient [3] -150.300, -100.000, -882.500
0333- ImagePositionPatient [3] -150.300, -100.000, -885.000
0334- ImagePositionPatient [3] -150.300, -100.000, -887.500
0335- ImagePositionPatient [3] -150.300, -100.000, -890.000
M0336 ImagePositionPatient [3] -150.300, -100.000, -892.500
M0337 ImagePositionPatient [3] -150.300, -100.000, -895.000
M0338 ImagePositionPatient [3] -150.300, -100.000, -897.500
M0339 ImagePositionPatient [3] -150.300, -100.000, -900.000
M0340 ImagePositionPatient [3] -150.300, -100.000, -902.500
0341- ImagePositionPatient [3] -150.300, -100.000, -905.000
0342- ImagePositionPatient [3] -150.300, -100.000, -907.500
M0343 ImagePositionPatient [3] -150.300, -100.000, -910.000
M0344 ImagePositionPatient [3] -150.300, -100.000, -912.500
M0345 ImagePositionPatient [3] -150.300, -100.000, -915.000
M0346 ImagePositionPatient [3] -150.300, -100.000, -917.500
M0347 ImagePositionPatient [3] -150.300, -100.000, -920.000
M0348 ImagePositionPatient [3] -150.300, -100.000, -922.500

In DICOM data sets, file names are ignored. Image slices are placed in position and orientation prescribed by “image position patient” and “image orientation patient” fields embedded in the file.

If slices are not spaced equally then you have no other option than enabling regularization. If there are artifacts then most probably the frames contain inconsistent information (image content is not consistent with its position and orientation). You may inspect the files using DICOM browser / Metadata feature to identify offending frames, remove them, clear the database, and re-import the data set without the inconsistent frames.

Thanks very much. I’ll go through this process then.
appriciate your feedbacks, helps a lot.
JR

@lassoan, I tried to have a look but didn’t find anything satisfying. However I really don’t understand why Slicer is trying to reconstruct something beetween -91,5 / - 383,250 and -538.250 / -792.5 as there is no slices. may be I misunderstand what he is doing…
Finaly the “harden transform” and and the “segment editor” are impossible to use. Slicer freezes everytime I lunch theses module with this scene. Normaly it works perfectly.

Thanks again for your insights,
Sincerely,

JR