[MINC-users] mincresample -like problem
Jérôme Redouté
redoute at cermep.fr
Wed Jun 7 11:21:56 EDT 2017
Hi Robert,
the output of mincresample is not coregistered anymore with previous files
here is the output of mincheader:
> mincheader BENSU_DPN_DYN_37F_sum.mnc
> hdf5 BENSU_DPN_DYN_37F_sum {
> dimensions:
> xspace = 256 ;
> yspace = 256 ;
> zspace = 109 ;
> variables:
> short image(zspace, yspace, xspace) ;
> image:version = "MINC Version 1.0" ;
> image:vartype = "group________" ;
> image:valid_range = 0., 65535. ;
> image:varid = "MINC standard variable" ;
> image:complete = "true_" ;
> image:dimorder = "zspace,yspace,xspace" ;
> image:signtype = "unsigned" ;
> double image-min(zspace) ;
> image-min:version = "MINC Version 1.0" ;
> image-min:vartype = "var_attribute" ;
> image-min:varid = "MINC standard variable" ;
> image-min:dimorder = "zspace" ;
> double image-max(zspace) ;
> image-max:version = "MINC Version 1.0" ;
> image-max:vartype = "var_attribute" ;
> image-max:varid = "MINC standard variable" ;
> image-max:dimorder = "zspace" ;
> double xspace ;
> xspace:version = "MINC Version 1.0" ;
> xspace:spacetype = "native____" ;
> xspace:vartype = "dimension____" ;
> xspace:start = -135. ;
> xspace:spacing = "irregular" ;
> xspace:alignment = "centre" ;
> xspace:direction_cosines = 1., 0., -0. ;
> xspace:comments = "X increases from patient left to right" ;
> xspace:varid = "MINC standard variable" ;
> xspace:length = 256 ;
> xspace:step = 1.06063 ;
> double yspace ;
> yspace:version = "MINC Version 1.0" ;
> yspace:spacetype = "native____" ;
> yspace:vartype = "dimension____" ;
> yspace:start = -135. ;
> yspace:spacing = "irregular" ;
> yspace:alignment = "centre" ;
> yspace:direction_cosines = 0., 1., -0. ;
> yspace:comments = "Y increases from patient posterior to
> anterior" ;
> yspace:varid = "MINC standard variable" ;
> yspace:length = 256 ;
> yspace:step = 1.06063 ;
> double zspace ;
> zspace:version = "MINC Version 1.0" ;
> zspace:spacetype = "native____" ;
> zspace:vartype = "dimension____" ;
> zspace:start = 127. ;
> zspace:spacing = "irregular" ;
> zspace:alignment = "centre" ;
> zspace:direction_cosines = 0., 0., 1. ;
> zspace:comments = "Z increases from patient inferior to
> superior" ;
> zspace:varid = "MINC standard variable" ;
> zspace:length = 109 ;
> zspace:step = -2.027 ;
> int acquisition ;
> acquisition:version = "MINC Version 1.0" ;
> acquisition:acquisition_id = "7" ;
> acquisition:vartype = "group________" ;
> acquisition:slice_thickness = 2.027 ;
> acquisition:injection_route = "\ufffd\ufffd@" ;
> acquisition:injection_minute = 0 ;
> acquisition:window_width = 1. ;
> acquisition:series_time = "143111.000000 " ;
> acquisition:injection_dose = 6.95309811585881e-310 ;
> acquisition:num_dyn_scans = 0. ;
> acquisition:injection_seconds = 0. ;
> acquisition:series_description = "DIPRE_DYN_UHD_12_21_Z3_256" ;
> acquisition:delay_in_TR = 0. ;
> acquisition:acquisition_time = "143111.000004 " ;
> acquisition:comments = "AC CT Brain, Volume Scaled" ;
> acquisition:image_time = "132439.593000 " ;
> acquisition:injection_day = 0 ;
> acquisition:tracer = "YNr" ;
> acquisition:injection_hour = 0 ;
> acquisition:radionuclide_halflife = 6.95098988200896e-310 ;
> acquisition:positron_fraction = 6.95098865937855e-310 ;
> acquisition:injection_year = 0 ;
> acquisition:varid = "MINC standard variable" ;
> acquisition:injection_volume = 6.95098935489284e-310 ;
> acquisition:dose_units = "Bq" ;
> acquisition:injection_time = "\b\ufffd\ufffd\ufffd" ;
> acquisition:image_type = "ORIGINAL\\PRIMARY" ;
> acquisition:start_time = "20151105 135819.250000 " ;
> acquisition:window_center = 0. ;
> acquisition:injection_month = 0 ;
> int dicom_0x0008 ;
> dicom_0x0008:el_0x0018 =
> "1.3.12.2.1107.5.1.4.11020.30000015112009095703100004143" ;
> dicom_0x0008:el_0x1090 = "SOMATOM Definition AS_mCT " ;
> dicom_0x0008:el_0x0021 = "20151105" ;
> dicom_0x0008:vartype = "group________" ;
> dicom_0x0008:el_0x0000 = 856 ;
> dicom_0x0008:el_0x1010 = "CTAWP71108" ;
> dicom_0x0008:el_0x0030 = "135819.250000 " ;
> dicom_0x0008:el_0x1030 = "PET^PETCT_Brain_LM_DIPRE (Adult)" ;
> dicom_0x0008:el_0x0031 = "143111.000000 " ;
> dicom_0x0008:el_0x0020 = "20151105" ;
> dicom_0x0008:el_0x103e = "DIPRE_DYN_UHD_12_21_Z3_256" ;
> dicom_0x0008:el_0x0080 = "CERMEP" ;
> dicom_0x0008:el_0x0022 = "20151105" ;
> dicom_0x0008:el_0x0060 = "PT" ;
> dicom_0x0008:el_0x0016 = "1.2.840.10008.5.1.4.1.1.128" ;
> dicom_0x0008:el_0x0070 = "SIEMENS " ;
> dicom_0x0008:varid = "MNI DICOM variable" ;
> dicom_0x0008:el_0x1250 = -2b, -1b, 0b, -32b, 38b, 1b, 0b, 0b,
> 32b, 0b, 0b, 0b, 4b, 0b, 0b, 0b, -128b, 0b, 0b, 0b, 32b, 0b, 13b, 0b,
> 56b, 0b, 0b, 0b, 49b, 46b, 51b, 46b, 49b, 50b, 46b, 50b, 46b, 49b,
> 49b, 48b, 55b, 46b, 53b, 46b, 49b, 46b, 52b, 46b, 49b, 49b, 48b, 50b,
> 48b, 46b, 51b, 48b, 48b, 48b, 48b, 48b, 49b, 53b, 49b, 49b, 48b, 53b,
> 48b, 55b, 51b, 55b, 48b, 56b, 48b, 57b, 51b, 48b, 48b, 48b, 48b, 48b,
> 48b, 48b, 57b, 0b, 32b, 0b, 14b, 0b, 56b, 0b, 0b, 0b, 49b, 46b, 51b,
> 46b, 49b, 50b, 46b, 50b, 46b, 49b, 49b, 48b, 55b, 46b, 53b, 46b, 49b,
> 46b, 52b, 46b, 49b, 49b, 48b, 50b, 48b, 46b, 51b, 48b, 48b, 48b, 48b,
> 48b, 49b, 53b, 49b, 49b, 49b, 57b, 48b, 56b, 50b, 55b, 51b, 51b, 51b,
> 49b, 50b, 48b, 48b, 48b, 49b, 48b, 49b, 55b, 50b, 0b, 64b, 0b, 0b, 0b,
> 4b, 0b, 0b, 0b, -114b, 0b, 0b, 0b, 64b, 0b, 112b, -95b, -122b, 0b, 0b,
> 0b, -2b, -1b, 0b, -32b, 126b, 0b, 0b, 0b, 8b, 0b, 0b, 0b, 4b, 0b, 0b,
> 0b, 114b, 0b, 0b, 0b, 8b, 0b, 0b, 1b, 6b, 0b, 0b, 0b, 49b, 50b, 50b,
> 52b, 48b, 51b, 8b, 0b, 2b, 1b, 4b, 0b, 0b, 0b, 68b, 67b, 77b, 32b, 8b,
> 0b, 4b, 1b, 26b, 0b, 0b, 0b, 70b, 111b, 114b, 32b, 65b, 116b, 116b,
> 101b, 110b, 117b, 97b, 116b, 105b, 111b, 110b, 32b, 67b, 111b, 114b,
> 114b, 101b, 99b, 116b, 105b, 111b, 110b, 8b, 0b, 5b, 1b, 4b, 0b, 0b,
> 0b, 68b, 67b, 77b, 82b, 8b, 0b, 6b, 1b, 22b, 0b, 0b, 0b, 50b, 48b,
> 48b, 51b, 48b, 54b, 49b, 57b, 48b, 48b, 48b, 48b, 48b, 48b, 46b, 48b,
> 48b, 48b, 48b, 48b, 48b, 32b, 8b, 0b, 15b, 1b, 4b, 0b, 0b, 0b, 55b,
> 50b, 49b, 48b ;
> dicom_0x0008:el_0x0008 = "ORIGINAL\\PRIMARY" ;
> dicom_0x0008:el_0x0005 = "ISO_IR 100" ;
> dicom_0x0008:el_0x0023 = "20151120" ;
> dicom_0x0008:el_0x0081 = "Bron Cedex /B7913E/ 69677 Boulevard
> Pinel 59" ;
> dicom_0x0008:el_0x1040 = "Department" ;
> dicom_0x0008:el_0x0032 = "143111.000004 " ;
> dicom_0x0008:el_0x0033 = "132439.593000 " ;
> int dicom_0x0010 ;
> dicom_0x0010:el_0x0010 = "BENSU06591" ;
> dicom_0x0010:vartype = "group________" ;
> dicom_0x0010:el_0x0000 = 100 ;
> dicom_0x0010:el_0x1010 = "023Y" ;
> dicom_0x0010:el_0x0030 = "19920101" ;
> dicom_0x0010:el_0x1030 = "54" ;
> dicom_0x0010:el_0x0040 = "F " ;
> dicom_0x0010:el_0x0020 = "BENSU ESTOUR DPN SPORTIFS " ;
> dicom_0x0010:varid = "MNI DICOM variable" ;
> int dicom_0x0018 ;
> dicom_0x0018:el_0x1020 = "syngo MI.PET/CT 2012A " ;
> dicom_0x0018:vartype = "group________" ;
> dicom_0x0018:el_0x5100 = "HFS " ;
> dicom_0x0018:el_0x1181 = "NONE" ;
> dicom_0x0018:el_0x1210 = "All-pass" ;
> dicom_0x0018:el_0x1000 = "11020 " ;
> dicom_0x0018:el_0x0000 = 174 ;
> dicom_0x0018:el_0x1242 = "20000 " ;
> dicom_0x0018:el_0x1201 = "081350.000000\\141756.000000 " ;
> dicom_0x0018:el_0x0050 = "2.027 " ;
> dicom_0x0018:varid = "MNI DICOM variable" ;
> dicom_0x0018:el_0x1200 = "20151105\\20150601 " ;
> int dicom_0x0020 ;
> dicom_0x0020:el_0x4000 = "AC CT Brain, Volume Scaled" ;
> dicom_0x0020:el_0x0010 = "1 " ;
> dicom_0x0020:vartype = "group________" ;
> dicom_0x0020:el_0x000d =
> "1.3.12.2.1107.5.1.4.11020.30000015110507370809300000009" ;
> dicom_0x0020:el_0x0000 = 356 ;
> dicom_0x0020:el_0x0012 = "2001" ;
> dicom_0x0020:el_0x1041 = "-439.729" ;
> dicom_0x0020:el_0x1001 = "0 " ;
> dicom_0x0020:el_0x0013 = "1 " ;
> dicom_0x0020:el_0x000e =
> "1.3.12.2.1107.5.1.4.11020.30000015112009095703100008067" ;
> dicom_0x0020:el_0x0011 = "7 " ;
> dicom_0x0020:varid = "MNI DICOM variable" ;
> dicom_0x0020:el_0x0052 =
> "1.3.12.2.1107.5.1.4.11020.30000015110507371409300000019" ;
> dicom_0x0020:el_0x0032 = "-136.82\\-371.453\\-439.729 " ;
> dicom_0x0020:el_0x0037 = "1\\0\\0\\0\\1\\0 " ;
> int dicom_0x0021 ;
> dicom_0x0021:vartype = "group________" ;
> dicom_0x0021:el_0x0000 = 30 ;
> dicom_0x0021:el_0x1370 = "0 " ;
> dicom_0x0021:el_0x1330 = "1 " ;
> dicom_0x0021:varid = "MNI DICOM variable" ;
> dicom_0x0021:el_0x1340 = "0 " ;
> int dicom_0x0023 ;
> dicom_0x0023:vartype = "group________" ;
> dicom_0x0023:el_0x0000 = 24 ;
> dicom_0x0023:el_0x0006 = "\ufffdYt\ufffd\ufffd" ;
> dicom_0x0023:varid = "MNI DICOM variable" ;
> dicom_0x0023:el_0x0008 = "0 " ;
> int dicom_0x0028 ;
> dicom_0x0028:el_0x0010 = 256s ;
> dicom_0x0028:vartype = "group________" ;
> dicom_0x0028:el_0x0004 = "MONOCHROME2 " ;
> dicom_0x0028:el_0x0103 = 0s ;
> dicom_0x0028:el_0x0000 = 236 ;
> dicom_0x0028:el_0x1054 = "BQML" ;
> dicom_0x0028:el_0x0100 = 16s ;
> dicom_0x0028:el_0x0102 = 15b, 0b ;
> dicom_0x0028:el_0x0030 = "1.06063\\1.06063 " ;
> dicom_0x0028:el_0x1053 = "34.968733588672 " ;
> dicom_0x0028:el_0x0107 = 0b, 0b ;
> dicom_0x0028:el_0x0106 = 0b, 0b ;
> dicom_0x0028:el_0x0051 = "NORM\\DTIM\\ATTN\\SCAT\\DECY\\RAN" ;
> dicom_0x0028:el_0x1052 = "0 " ;
> dicom_0x0028:el_0x0011 = 256s ;
> dicom_0x0028:varid = "MNI DICOM variable" ;
> dicom_0x0028:el_0x0101 = 16s ;
> dicom_0x0028:el_0x1050 = "0 " ;
> dicom_0x0028:el_0x1051 = "1 " ;
> dicom_0x0028:el_0x0002 = 1b, 0b ;
> int dicom_0x0029 ;
> dicom_0x0029:el_0x0010 = "SIEMENS CSA HEADER" ;
> dicom_0x0029:el_0x1020 =
> "<pds><com>gm:1104,236,0,0,go:-1.059,0.308,754.271,0.042,0.038,0.001,QC:1,1,0,101.8,39.6,31.7,0,1,0,0.2,0.8,0,3.109e+007,zo:3,xO:0,yO:0,CT:1.3.12.2.1107.5.1.4.11020.30000015111908273331200010172</com><dat><fg>1.3.12.2.1107.5.1.4.11020.30000015110508273160900000065,DFDef:0,0,20-1,20,40-2,40,60-3,60,80-4,80,100-5,100,120-6,120,140-7,140,160-8,160,180-9,180,200-10,200,220-11,220,240-12,240,260-13,260,280-14,280,300-15,300,420-16,420,540-17,540,660-18,660,780-19,780,900-20,900,1020-21,1020,1140-22,1140,1260-23,1260,1380-24,1380,1500-25,1500,1620-26,1620,1740-27,1740,1860-28,1860,1980-29,1980,2100-30,2100,2400-31,2400,2700-32,2700,3000-33,3000,3300-34,3300,3600-35,3600,3900-36,3900,4200-</fg></dat></pds>\r\n",
> "" ;
> dicom_0x0029:vartype = "group________" ;
> dicom_0x0029:el_0x0000 = 780 ;
> dicom_0x0029:varid = "MNI DICOM variable" ;
> dicom_0x0029:el_0x1018 = "PET_REPLAY_PARAM" ;
> dicom_0x0029:el_0x1019 = "1.3 " ;
> int dicom_0x0054 ;
> dicom_0x0054:el_0x0410 = -2b, -1b, 0b, -32b, -8b, 0b, 0b, 0b,
> 8b, 0b, 0b, 0b, 4b, 0b, 0b, 0b, 100b, 0b, 0b, 0b, 8b, 0b, 0b, 1b, 8b,
> 0b, 0b, 0b, 70b, 45b, 49b, 48b, 52b, 53b, 48b, 32b, 8b, 0b, 2b, 1b,
> 6b, 0b, 0b, 0b, 57b, 57b, 83b, 68b, 77b, 32b, 8b, 0b, 4b, 1b, 10b, 0b,
> 0b, 0b, 114b, 101b, 99b, 117b, 109b, 98b, 101b, 110b, 116b, 32b, 8b,
> 0b, 5b, 1b, 4b, 0b, 0b, 0b, 68b, 67b, 77b, 82b, 8b, 0b, 6b, 1b, 22b,
> 0b, 0b, 0b, 50b, 48b, 48b, 50b, 48b, 57b, 48b, 52b, 48b, 48b, 48b,
> 48b, 48b, 48b, 46b, 48b, 48b, 48b, 48b, 48b, 48b, 32b, 8b, 0b, 15b,
> 1b, 2b, 0b, 0b, 0b, 49b, 57b, 84b, 0b, 0b, 0b, 4b, 0b, 0b, 0b, 124b,
> 0b, 0b, 0b, 84b, 0b, 18b, 4b, 116b, 0b, 0b, 0b, -2b, -1b, 0b, -32b,
> 108b, 0b, 0b, 0b, 8b, 0b, 0b, 0b, 4b, 0b, 0b, 0b, 96b, 0b, 0b, 0b, 8b,
> 0b, 0b, 1b, 8b, 0b, 0b, 0b, 70b, 45b, 49b, 48b, 51b, 52b, 48b, 32b,
> 8b, 0b, 2b, 1b, 6b, 0b, 0b, 0b, 57b, 57b, 83b, 68b, 77b, 32b, 8b, 0b,
> 4b, 1b, 6b, 0b, 0b, 0b, 115b, 117b, 112b, 105b, 110b, 101b, 8b, 0b,
> 5b, 1b, 4b, 0b, 0b, 0b, 68b, 67b, 77b, 82b, 8b, 0b, 6b, 1b, 22b, 0b,
> 0b, 0b, 50b, 48b, 48b, 50b, 48b, 57b, 48b, 52b, 48b, 48b, 48b, 48b,
> 48b, 48b, 46b, 48b, 48b, 48b, 48b, 48b, 48b, 32b, 8b, 0b, 15b, 1b, 2b,
> 0b, 0b, 0b, 50b, 48b ;
> dicom_0x0054:el_0x1105 = "Model-based " ;
> dicom_0x0054:el_0x1300 = "9990.5540141915 " ;
> dicom_0x0054:vartype = "group________" ;
> dicom_0x0054:el_0x0414 = -2b, -1b, 0b, -32b, 112b, 0b, 0b, 0b,
> 8b, 0b, 0b, 0b, 4b, 0b, 0b, 0b, 100b, 0b, 0b, 0b, 8b, 0b, 0b, 1b, 8b,
> 0b, 0b, 0b, 70b, 45b, 49b, 48b, 52b, 55b, 48b, 32b, 8b, 0b, 2b, 1b,
> 6b, 0b, 0b, 0b, 57b, 57b, 83b, 68b, 77b, 32b, 8b, 0b, 4b, 1b, 10b, 0b,
> 0b, 0b, 104b, 101b, 97b, 100b, 102b, 105b, 114b, 115b, 116b, 32b, 8b,
> 0b, 5b, 1b, 4b, 0b, 0b, 0b, 68b, 67b, 77b, 82b, 8b, 0b, 6b, 1b, 22b,
> 0b, 0b, 0b, 50b, 48b, 48b, 50b, 48b, 57b, 48b, 52b, 48b, 48b, 48b,
> 48b, 48b, 48b, 46b, 48b, 48b, 48b, 48b, 48b, 48b, 32b, 8b, 0b, 15b,
> 1b, 2b, 0b, 0b, 0b, 50b, 49b ;
> dicom_0x0054:el_0x1101 = "measured,AC CT Brain" ;
> dicom_0x0054:el_0x1000 = "DYNAMIC\\IMAGE " ;
> dicom_0x0054:el_0x1322 = "31086800" ;
> dicom_0x0054:el_0x1102 = "START " ;
> dicom_0x0054:el_0x0000 = 964 ;
> dicom_0x0054:el_0x1100 = "DLYD" ;
> dicom_0x0054:el_0x1321 = "1.00568 " ;
> dicom_0x0054:el_0x1001 = "BQML" ;
> dicom_0x0054:el_0x1201 = "5\\6 " ;
> dicom_0x0054:el_0x0013 = -2b, -1b, 0b, -32b, 36b, 0b, 0b, 0b,
> 84b, 0b, 0b, 0b, 4b, 0b, 0b, 0b, 24b, 0b, 0b, 0b, 84b, 0b, 20b, 0b,
> 4b, 0b, 0b, 0b, 52b, 51b, 53b, 32b, 84b, 0b, 21b, 0b, 4b, 0b, 0b, 0b,
> 54b, 53b, 48b, 32b ;
> dicom_0x0054:el_0x0016 =
> "\ufffd\ufffd\ufffd\ufffdN1\bSolutionr143000.000000 t\n",
> "177380000 u1223v1
> T\ufffdTx\ufffd\ufffd\ufffdp\bd\b\bC-105A1 \bSRT \b\n",
> "^11^Carbon\bDCMR\b20070625000000.000000 \b4020" ;
> dicom_0x0054:el_0x1330 = 1s ;
> dicom_0x0054:varid = "MNI DICOM variable" ;
> dicom_0x0054:el_0x1323 = "0.322837" ;
> dicom_0x0054:el_0x0081 = 109s ;
> dicom_0x0054:el_0x1002 = "EMISSION" ;
> dicom_0x0054:el_0x0101 = 37s ;
> dicom_0x0054:el_0x1200 = "49" ;
> dicom_0x0054:el_0x1103 = "PSF+TOF 12i21s" ;
> int dicom_0x0071 ;
> dicom_0x0071:el_0x0010 = "SIEMENS MED PT" ;
> dicom_0x0071:vartype = "group________" ;
> dicom_0x0071:el_0x0000 = 52 ;
> dicom_0x0071:el_0x1022 = "20151105143111.000000 " ;
> dicom_0x0071:varid = "MNI DICOM variable" ;
> int dicom_groups ;
> dicom_groups:vartype = "group________" ;
> dicom_groups:varid = "MNI DICOM variable" ;
> int dicominfo ;
> dicominfo:vartype = "group________" ;
> dicominfo:window_min = -0.5 ;
> dicominfo:varid = "MNI DICOM information variable" ;
> dicominfo:window_max = 1145820. ;
> dicominfo:image_type = "ORIGINAL\\PRIMARY" ;
> int patient ;
> patient:version = "MINC Version 1.0" ;
> patient:full_name = "BENSU06591" ;
> patient:vartype = "group________" ;
> patient:age = 23. ;
> patient:weight = 54. ;
> patient:birthdate = "19920101" ;
> patient:position = "HFS " ;
> patient:sex = "female" ;
> patient:identification = "BENSU ESTOUR DPN SPORTIFS " ;
> patient:varid = "MINC standard variable" ;
> int study ;
> study:serial_no = "11020 " ;
> study:procedure = "PET^PETCT_Brain_LM_DIPRE (Adult)" ;
> study:station_id = "CTAWP71108" ;
> study:study_id = "20151104.135819" ;
> study:software_version = "syngo MI.PET/CT 2012A " ;
> study:version = "MINC Version 1.0" ;
> study:vartype = "group________" ;
> study:calibration_time = "081350.000000\\141756.000000 " ;
> study:institution = "CERMEP" ;
> study:modality = "PET__" ;
> study:start_date = "20151105" ;
> study:device_model = "SOMATOM Definition AS_mCT " ;
> study:varid = "MINC standard variable" ;
> study:calibration_date = "20151105\\20150601 " ;
> study:manufacturer = "SIEMENS " ;
> study:start_time = "135819.250000 " ;
>
> // global attributes:
> :ident = "redoute:apollon:2017.06.07.16.34.56:19987:1" ;
> :minc_version = "2.4.02" ;
> :history = "Wed Jun 7 16:29:42 2017>>> dcm2mnc
> -adjust_frame_time -dname -fname BENSU_DPN_DYN_37F
> /home/chuste/SPORTIVES_DPN/DICOM/BENSU/BENSU_DPN_DYN ./\n",
> "Wed Jun 7 16:29:56 2017>>> mincreshape +xdirection
> +ydirection +zdirection BENSU_DPN_DYN_37F.mnc TMP.mnc\n",
> "Wed Jun 7 16:34:56 2017>>> mincaverage -avgdim time
> /home/redoute/protocoles/TEP/SPORTIVES/DATA/BENSU/BENSU_DPN_DYN_37F.mnc
> /home/redoute/protocoles/TEP/SPORTIVES/DATA/BENSU/BENSU_DPN_DYN_37F_sum.mnc\n",
> "" ;
> data:
>
> image-min = 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ;
>
> image-max = 1015.97951002534, 1240.91749194396, 630.382305503898,
> 723.002194468489, 511.299591120853, 450.813133021528,
> 410.170996250848,
> 336.455923177493, 332.677163576246, 350.630994662977,
> 544.378295949706,
> 338.345692353633, 487.672068425804, 521.697085552957,
> 431.911158129436,
> 770.256821640438, 2799.38299059135, 7770.62034174942,
> 8482.28947336752,
> 7311.29238818473, 8237.5266244748, 8216.71158998212,
> 7388.81507791155,
> 6908.67382041203, 6631.77800213614, 13994.1722639211,
> 25789.0164509082,
> 23597.3480681966, 22800.5333269836, 27038.4614541529,
> 24876.0739949538,
> 23241.9655096776, 23723.9253238975, 23875.1954337083,
> 23959.2471432625,
> 25403.3672287019, 26914.6309831411, 26450.5532251209,
> 26689.7233004063,
> 28028.9090779358, 27474.0787172964, 24943.1621707318,
> 26341.8762397411,
> 27439.9909818683, 28157.3802273092, 28828.315531433,
> 27267.0795538751,
> 27136.666213844, 27628.9816285747, 26338.0979560432,
> 25649.1439537558,
> 24497.976667637, 25563.0949208548, 31710.9625537502,
> 28759.5265633965,
> 29021.1731529272, 26897.6213588406, 26410.8196023807,
> 29460.6965591512,
> 28964.4353283011, 27777.4142003581, 28767.9773100351, 26587.64885472,
> 28103.502048587, 26836.0683435148, 25409.0242348483,
> 26819.1750127021,
> 25862.6754683284, 27790.6644761479, 26720.8615018712,
> 29452.1399744785,
> 86457.7847388781, 96697.9745770936, 27089.5121032407,
> 26246.2997936328,
> 26895.6974255682, 28537.3314435693, 24599.9965574869,
> 27394.7222563613,
> 27130.0692263568, 22924.2698431253, 21530.3207497954,
> 14907.0967220738,
> 16521.2481834412, 16741.6011532759, 16129.122218676,
> 14679.4045717525,
> 17194.2099996542, 15261.4439887782, 15532.7040867694,
> 16324.6789335692,
> 12881.7204989359, 10639.9370643974, 11762.7352867794,
> 11214.4996639019,
> 12202.2473434282, 11111.5606026694, 15651.7596746581,
> 13704.0686550507,
> 13669.0525041769, 16991.0475695223, 16069.6059257307,
> 15393.7603655957,
> 16025.2247745041, 15350.2913481498, 21429.1910733267,
> 25955.3927300149,
> 36845.5970575126, 37132.9700624098 ;
>
> xspace = 0 ;
>
> yspace = 0 ;
>
> zspace = 0 ;
>
> acquisition = 0 ;
>
> dicom_0x0008 = 0 ;
>
> dicom_0x0010 = 0 ;
>
> dicom_0x0018 = 0 ;
>
> dicom_0x0020 = 0 ;
>
> dicom_0x0021 = 0 ;
>
> dicom_0x0023 = 0 ;
>
> dicom_0x0028 = 0 ;
>
> dicom_0x0029 = 0 ;
>
> dicom_0x0054 = 0 ;
>
> dicom_0x0071 = 0 ;
>
> dicom_groups = 0 ;
>
> dicominfo = 0 ;
>
> patient = 0 ;
>
> study = 0 ;
> }
Le 07/06/2017 à 17:08, Robert D. Vincent a écrit :
> Hi Jerome,
>
> I'm not sure. Those warnings may not be telling us anything important. Does
> the output of mincresample look good?
>
> Can you send the output of mincheader for TEP_sum.mnc?
>
> -bert
>
> On Wed, Jun 7, 2017 at 10:51 AM, Jérôme Redouté <redoute at cermep.fr> wrote:
>
>> Hi all,
>>
>> here is the problem we are facing with:
>>
>> 1. dcm2mnc DICOM to TEP_DYN.mnc
>>
>> 2. mincaverage -avgdim time TEP_DYN.mnc TEP_sum.mnc
>>
>> 3. mnc2nii TEP_sum.mnc TEP_sum.nii
>>
>> 3. we use SPM to coregister TEP_sum.nii with MRI, segment MRI and then
>> push ATLAS.nii in TEP_sum space
>>
>> 4. at this point: ATLAS.nii and TEP_sum.nii are well coregistred when
>> checking with register
>>
>> 5. nii2mnc -byte ATLAS.nii ATLAS.mnc
>>
>> 6. then we need to resample ATLAS.mnc:
>>
>> mincresample -verbose -nearest_neighbour -byte -like TEP_sum.mnc
>> ATLAS.mnc ATLAS_Res.mnc
>>
>> the problem is at this step:
>>
>> we get warnings:
>>
>> WARN: Irregular dimension in file TEP_sum.mnc contains non-monotonic or
>>> repeated values.
>>> WARN: Something is wrong with the irregular dimension in file TEP_sum.mnc.
>>> Substituting a step size of 1.0.
>>> WARN: Irregular dimension in file EP_sum.mnc contains non-monotonic or
>>> repeated values.
>>> WARN: Something is wrong with the irregular dimension in file EP_sum.mnc.
>>> Substituting a step size of 1.0.
>>> WARN: Irregular dimension in file EP_sum.mnc contains non-monotonic or
>>> repeated values.
>>> WARN: Something is wrong with the irregular dimension in file EP_sum.mnc.
>>> Substituting a step size of 1.0.
>>>
>> and the resulting ATLAS_Res.mnc is not coregistred with TEP_sum.mnc
>>
>> Any ideas n what is wrong with our reference image?
>>
>> thank you
>>
>> Jerome
>>
>>
>>
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
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