From AMORALESPINZON at bwh.harvard.edu Wed Jun 17 13:29:17 2020 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Wed, 17 Jun 2020 17:29:17 +0000 Subject: [Loris-dev] Issue dcm2mnc z_space=1 Message-ID: <61932DF2-8E8C-4797-96BB-607874AC4721@bwh.harvard.edu> Dear LorisDev team, We are facing an issue with some Dicoms (~400 Dicom studies) being converted to minc files having only one slide (z_space=1) when importing them in LORIS. This issue however seems to be happening in the version 2.3.01 of dcm2mnc used by LORIS: === $ dcm2mnc -version program: 2.3.01 built Jan 17 2018 17:39:49 libminc: 2.4.02 netcdf : 4.5.0 of Jan 17 2018 17:09:58 $ HDF5 : 1.8.20 === but not in version 2.0.07, which we have in a different environment: === $ dcm2mnc -version program: 2.0.07 built Oct 31 2017 14:03:56 libminc: 2.2.00 netcdf : 4.2.1 of Oct 31 2017 13:59:53 $ HDF5 : 1.8.8 === I am attaching the output I get when converting a set of Dicoms for one acquisition and also the mncheader of the created file. Do you know why this might be happening? I can share a deidentified testing Dicom if this helps. Regards, Alfredo. Output dcm2mnc: === $ dcm2mnc Dicom-pdw/ . Checking file types... File Dicom-pdw/000001.dcm appears to be DICOM (CD/Export). Parsing 60 files |<--------------------------------------------------->| Sorting 60 files... Done sorting files. Processing files, one series at a time... INFO: Number of distinct coordinates: 60 WARNING: Acquisition number is not informative. WARNING: Image number is a mystery. WARNING: Minimum image number is 4 WARNING: Temporal position identifier is useless. INFO: Acquisition number ranges from 1 to 1 INFO: Image number ranges from 4 to 63 INFO: Temporal position id ranges from -1 to -1. -Parsing series info |<--First Slice at 0,102.006497,0.000000 | First Echo at 1,0.012000,0.000000 First Time at 4,-61.117167,0.000000 First Phase at 1,0.000000,0.000000 First ChmSh at 1,0.000000,0.000000 Warning: merging extra indices on Time axis: 1 5 ->Warning: merging extra indices on Time axis: 1 6 ->Warning: merging extra indices on Time axis: 1 7 ->Warning: merging extra indices on Time axis: 1 8 ->Warning: merging extra indices on Time axis: 1 9 ->Warning: merging extra indices on Time axis: 1 10 Warning: merging extra indices on Time axis: 1 11 ->Warning: merging extra indices on Time axis: 1 12 ->Warning: merging extra indices on Time axis: 1 13 ->Warning: merging extra indices on Time axis: 1 14 ->Warning: merging extra indices on Time axis: 1 15 ->Warning: merging extra indices on Time axis: 1 16 ->Warning: merging extra indices on Time axis: 1 17 Warning: merging extra indices on Time axis: 1 18 ->Warning: merging extra indices on Time axis: 1 19 ->Warning: merging extra indices on Time axis: 1 20 ->Warning: merging extra indices on Time axis: 1 21 ->Warning: merging extra indices on Time axis: 1 22 ->Warning: merging extra indices on Time axis: 1 23 Warning: merging extra indices on Time axis: 1 24 ->Warning: merging extra indices on Time axis: 1 25 ->Warning: merging extra indices on Time axis: 1 26 ->Warning: merging extra indices on Time axis: 1 27 ->Warning: merging extra indices on Time axis: 1 28 ->Warning: merging extra indices on Time axis: 1 29 ->Warning: merging extra indices on Time axis: 1 30 Warning: merging extra indices on Time axis: 1 31 ->Warning: merging extra indices on Time axis: 1 32 ->Warning: merging extra indices on Time axis: 1 33 ->Warning: merging extra indices on Time axis: 1 34 ->Warning: merging extra indices on Time axis: 1 35 ->Warning: merging extra indices on Time axis: 1 36 Warning: merging extra indices on Time axis: 1 37 ->Warning: merging extra indices on Time axis: 1 38 ->Warning: merging extra indices on Time axis: 1 39 ->Warning: merging extra indices on Time axis: 1 40 ->Warning: merging extra indices on Time axis: 1 41 ->Warning: merging extra indices on Time axis: 1 42 ->Warning: merging extra indices on Time axis: 1 43 Warning: merging extra indices on Time axis: 1 44 ->Warning: merging extra indices on Time axis: 1 45 ->Warning: merging extra indices on Time axis: 1 46 ->Warning: merging extra indices on Time axis: 1 47 ->Warning: merging extra indices on Time axis: 1 48 ->Warning: merging extra indices on Time axis: 1 49 Warning: merging extra indices on Time axis: 1 50 ->Warning: merging extra indices on Time axis: 1 51 ->Warning: merging extra indices on Time axis: 1 52 ->Warning: merging extra indices on Time axis: 1 53 ->Warning: merging extra indices on Time axis: 1 54 ->Warning: merging extra indices on Time axis: 1 55 ->Warning: merging extra indices on Time axis: 1 56 Warning: merging extra indices on Time axis: 1 57 ->Warning: merging extra indices on Time axis: 1 58 ->Warning: merging extra indices on Time axis: 1 59 ->Warning: merging extra indices on Time axis: 1 60 ->Warning: merging extra indices on Time axis: 1 61 ->Warning: merging extra indices on Time axis: 1 62 ->Warning: merging extra indices on Time axis: 1 63 WARNING: Age was not numeric!! -Creating minc file |<--------------------------------------------------->| Done processing files. === mnc header === $ mincheader abc.mnc hdf5 abc { dimensions: xspace = 256 ; yspace = 256 ; zspace = 1 ; variables: short image(zspace, yspace, xspace) ; image:version = "MINC Version 1.0" ; image:vartype = "group________" ; image:valid_range = 0., 4095. ; 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" ; int xspace ; xspace:version = "MINC Version 1.0" ; xspace:spacetype = "native____" ; xspace:vartype = "dimension____" ; xspace:start = 125. ; xspace:spacing = "regular__" ; 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 = -0.9765625 ; int yspace ; yspace:version = "MINC Version 1.0" ; yspace:spacetype = "native____" ; yspace:vartype = "dimension____" ; yspace:start = 114.989938629699 ; yspace:spacing = "regular__" ; yspace:alignment = "centre" ; yspace:direction_cosines = 0., 0.996194701817766, 0.0871557001590339 ; yspace:comments = "Y increases from patient posterior to anterior" ; yspace:varid = "MINC standard variable" ; yspace:length = 256 ; yspace:step = -0.9765625 ; double zspace ; zspace:version = "MINC Version 1.0" ; zspace:spacetype = "native____" ; zspace:vartype = "dimension____" ; zspace:start = 102.00649652328 ; zspace:spacing = "regular__" ; zspace:alignment = "centre" ; zspace:direction_cosines = -0., -0.0871557001590339, 0.996194701817766 ; zspace:comments = "Z increases from patient inferior to superior" ; zspace:varid = "MINC standard variable" ; zspace:length = 1 ; zspace:step = 3. ; int acquisition ; acquisition:version = "MINC Version 1.0" ; acquisition:scanning_sequence = "tse1-3" ; acquisition:percent_phase_fov = 100. ; acquisition:phase_enc_dir = "ROW " ; acquisition:acquisition_id = "2" ; acquisition:vartype = "group________" ; acquisition:slice_thickness = 3. ; acquisition:echo_number = 1. ; acquisition:imaging_frequency = 40461870. ; acquisition:injection_route = "" ; acquisition:injection_minute = 0 ; acquisition:window_width = 309. ; acquisition:series_time = "163538.580000 " ; acquisition:mr_acq_type = "2D" ; acquisition:num_dyn_scans = 1. ; acquisition:percent_sampling = 100. ; acquisition:SAR = 0. ; acquisition:injection_seconds = 0. ; acquisition:series_description = "pdw " ; acquisition:echo_train_length = 1. ; acquisition:repetition_time = 2.76 ; acquisition:acquisition_time = "163437.462833 " ; acquisition:comments = "Anonymized" ; acquisition:image_time = "163939.665000 " ; acquisition:num_averages = 1. ; acquisition:imaged_nucleus = "1H" ; acquisition:flip_angle = 180. ; acquisition:injection_day = 0 ; acquisition:tracer = "?????" ; acquisition:injection_hour = 0 ; acquisition:injection_year = 0 ; acquisition:varid = "MINC standard variable" ; acquisition:injection_volume = 4.94065645841247e-323 ; acquisition:injection_time = "\b" ; acquisition:image_type = "DERIVED\\SECONDARY\\OTHER " ; acquisition:start_time = "20090324 163029.686000 " ; acquisition:window_center = 131. ; acquisition:injection_month = 0 ; acquisition:receive_coil = "CP Head " ; acquisition:echo_time = 0.012 ; int dicom_0x0008 ; dicom_0x0008:el_0x0018 = "1.3.12.2.1107.5.2.2.9082.20090324163538000002004" ; dicom_0x0008:el_0x0090 = "Anonymized" ; dicom_0x0008:el_0x1090 = "MAGNETOM EXPERT " ; dicom_0x0008:el_0x0021 = "20090324" ; dicom_0x0008:vartype = "group________" ; dicom_0x0008:el_0x0000 = 524 ; dicom_0x0008:el_0x1010 = "Anonymized" ; dicom_0x0008:el_0x0030 = "163029.686000 " ; dicom_0x0008:el_0x0031 = "163538.580000 " ; dicom_0x0008:el_0x0020 = "20090324" ; dicom_0x0008:el_0x103e = "pdw " ; dicom_0x0008:el_0x0080 = "Anonymized" ; dicom_0x0008:el_0x0022 = "20090324" ; dicom_0x0008:el_0x0060 = "MR" ; dicom_0x0008:el_0x0016 = "1.2.840.10008.5.1.4.1.1.4" ; dicom_0x0008:el_0x0070 = "SIEMENS " ; dicom_0x0008:el_0x2111 = "Lossless JPEG compression, selection value 1, point transform 0, compression ratio 1.5987 " ; dicom_0x0008:el_0x0050 = "Anonymized" ; dicom_0x0008:varid = "MNI DICOM variable" ; dicom_0x0008:el_0x0008 = "DERIVED\\SECONDARY\\OTHER " ; dicom_0x0008:el_0x0005 = "ISO_IR 100" ; dicom_0x0008:el_0x0023 = "20090324" ; dicom_0x0008:el_0x0032 = "163437.462833 " ; dicom_0x0008:el_0x0033 = "163939.665000 " ; int dicom_0x0009 ; dicom_0x0009:el_0x0010 = "SPI RELEASE 1 " ; dicom_0x0009:vartype = "group________" ; dicom_0x0009:el_0x1210 = "STANDARD" ; dicom_0x0009:el_0x1227 = "163337.000000 " ; dicom_0x0009:el_0x0000 = 332 ; dicom_0x0009:el_0x1010 = "SPI VERSION 01.00 " ; dicom_0x0009:el_0x1320 = "VC" ; dicom_0x0009:el_0x0012 = "SIEMENS CM VA0 CMS " ; dicom_0x0009:el_0x1041 = "MRUPNONE" ; dicom_0x0009:el_0x1226 = "20090324" ; dicom_0x0009:el_0x1213 = " 0" ; dicom_0x0009:el_0x1214 = " 0" ; dicom_0x0009:el_0x0013 = "SIEMENS CM VA0 LAB " ; dicom_0x0009:el_0x1015 = "049S01MR012009032416400317" ; dicom_0x0009:varid = "MNI DICOM variable" ; dicom_0x0009:el_0x1316 = "728b43ed" ; dicom_0x0009:el_0x1212 = 0b, 0b, 0b, 0b ; dicom_0x0009:el_0x1040 = 0b, 0b ; int dicom_0x0010 ; dicom_0x0010:el_0x0010 = "ABC" ; dicom_0x0010:vartype = "group________" ; dicom_0x0010:el_0x0000 = 154 ; dicom_0x0010:el_0x1010 = "Anonymized" ; dicom_0x0010:el_0x0030 = "SA " ; dicom_0x0010:el_0x1030 = "57" ; dicom_0x0010:el_0x0040 = "Anonymized" ; dicom_0x0010:el_0x0020 = "ABC" ; dicom_0x0010:varid = "MNI DICOM variable" ; int dicom_0x0011 ; dicom_0x0011:el_0x0010 = "SPI RELEASE 1 " ; dicom_0x0011:vartype = "group________" ; dicom_0x0011:el_0x1123 = " 57" ; dicom_0x0011:el_0x0000 = 126 ; dicom_0x0011:el_0x1111 = "163029.686000 " ; dicom_0x0011:el_0x1110 = "20090324" ; dicom_0x0011:el_0x0011 = "SIEMENS CM VA0 CMS " ; dicom_0x0011:varid = "MNI DICOM variable" ; int dicom_0x0018 ; dicom_0x0018:el_0x0086 = " 1" ; dicom_0x0018:el_0x0021 = "NONE" ; dicom_0x0018:el_0x1020 = "VB33G " ; dicom_0x0018:el_0x0024 = "tse1-3" ; dicom_0x0018:vartype = "group________" ; dicom_0x0018:el_0x5100 = "HFS " ; dicom_0x0018:el_0x1000 = " 9082" ; dicom_0x0018:el_0x0000 = 420 ; dicom_0x0018:el_0x0091 = "1 " ; dicom_0x0018:el_0x0093 = "100 " ; dicom_0x0018:el_0x0094 = "100 " ; dicom_0x0018:el_0x0085 = "1H" ; dicom_0x0018:el_0x0083 = "1 " ; dicom_0x0018:el_0x1314 = "180 " ; dicom_0x0018:el_0x0087 = "0.9500702 " ; dicom_0x0018:el_0x1201 = "153242.000000 " ; dicom_0x0018:el_0x0020 = "RM" ; dicom_0x0018:el_0x0080 = "002.760000E+03" ; dicom_0x0018:el_0x1312 = "ROW " ; dicom_0x0018:el_0x0050 = "003.000000E+00" ; dicom_0x0018:el_0x1310 = 0s, 256s, 252s, 0s ; dicom_0x0018:varid = "MNI DICOM variable" ; dicom_0x0018:el_0x1250 = "CP Head " ; dicom_0x0018:el_0x1316 = "0 " ; dicom_0x0018:el_0x0023 = "2D" ; dicom_0x0018:el_0x0081 = "001.200000E+01" ; dicom_0x0018:el_0x1200 = "20050304" ; dicom_0x0018:el_0x0025 = "N " ; dicom_0x0018:el_0x0088 = "0 " ; dicom_0x0018:el_0x0084 = "004.046187E+01" ; int dicom_0x0019 ; dicom_0x0019:el_0x1296 = 1b, 39b, 0b, 0b, 1b, 39b, 0b, 0b, 2b, 0b, 0b, 0b ; dicom_0x0019:el_0x14d6 = " 0" ; dicom_0x0019:el_0x14a6 = "001.000000E+02\\04.348140E+00\\04.422564E+00" ; dicom_0x0019:el_0x1455 = "001.022977E+02" ; dicom_0x0019:el_0x1482 = "002.000000E+02" ; dicom_0x0019:el_0x1285 = "NONE " ; dicom_0x0019:el_0x14a2 = "001.034203E+00" ; dicom_0x0019:el_0x1245 = " 1" ; dicom_0x0019:el_0x1422 = "002.700000E+01" ; dicom_0x0019:el_0x0010 = "SIEMENS CM VA0 CMS " ; dicom_0x0019:el_0x1020 = "EXAMNONE" ; dicom_0x0019:vartype = "group________" ; dicom_0x0019:el_0x14a0 = " 1" ; dicom_0x0019:el_0x1211 = "002.388881E+02" ; dicom_0x0019:el_0x1294 = "001.570796E+00" ; dicom_0x0019:el_0x1471 = "004.698000E+00" ; dicom_0x0019:el_0x14d3 = "001.000000E+00" ; dicom_0x0019:el_0x1060 = "131072" ; dicom_0x0019:el_0x1297 = 64b, 8b, -64b, 1b, -22b, -76b, -1b, -1b ; dicom_0x0019:el_0x1210 = "002.388881E+02" ; dicom_0x0019:el_0x1472 = "008.000000E+00" ; dicom_0x0019:el_0x0000 = 1900 ; dicom_0x0019:el_0x1231 = " 256" ; dicom_0x0019:el_0x14da = "PLUSX " ; dicom_0x0019:el_0x1228 = " -126" ; dicom_0x0019:el_0x0015 = "SIEMENS CM VA0 ACQU" ; dicom_0x0019:el_0x1010 = " 50" ; dicom_0x0019:el_0x14d2 = "NONE" ; dicom_0x0019:el_0x0012 = "SIEMENS MR VA0 GEN " ; dicom_0x0019:el_0x1451 = "005.500000E+01" ; dicom_0x0019:el_0x14a5 = "001.500000E+00\\05.203557E-02\\00.000000E+00" ; dicom_0x0019:el_0x1230 = " 256" ; dicom_0x0019:el_0x0014 = "SIEMENS MR VA0 COAD" ; dicom_0x0019:el_0x1226 = " 125" ; dicom_0x0019:el_0x1512 = "SIEMENS " ; dicom_0x0019:el_0x1421 = " 2" ; dicom_0x0019:el_0x1030 = "A IRS " ; dicom_0x0019:el_0x1414 = "001.000000E+01" ; dicom_0x0019:el_0x1213 = "002.000000E+01" ; dicom_0x0019:el_0x1260 = "001.800000E+02" ; dicom_0x0019:el_0x1298 = "000.000000E+00\\00.000000E+00\\00.000000E+00" ; dicom_0x0019:el_0x14d5 = " 0" ; dicom_0x0019:el_0x1456 = " 25000" ; dicom_0x0019:el_0x1454 = "-01.000000E+00" ; dicom_0x0019:el_0x1240 = " 0" ; dicom_0x0019:el_0x1460 = "006.025031E-01" ; dicom_0x0019:el_0x1420 = "001.660000E+02" ; dicom_0x0019:el_0x1470 = "004.698000E+00" ; dicom_0x0019:el_0x1424 = "003.908454E+01" ; dicom_0x0019:el_0x1510 = "/usr/appl/proto/014/c/head/LAQ302/PDW_AX.prg" ; dicom_0x0019:el_0x1290 = " 0" ; dicom_0x0019:el_0x1480 = "001.430000E+02\\01.570000E+02\\01.450000E+02" ; dicom_0x0019:el_0x1221 = " 252" ; dicom_0x0019:el_0x1450 = "008.900000E+01" ; dicom_0x0019:el_0x1220 = " 252" ; dicom_0x0019:el_0x1426 = "006.584084E+01" ; dicom_0x0019:el_0x1214 = " 1" ; dicom_0x0019:el_0x14d8 = " 129" ; dicom_0x0019:el_0x1216 = 1b, 1b, 69b, 0b, 64b, 0b, 0b, 0b ; dicom_0x0019:el_0x1281 = "NONE " ; dicom_0x0019:el_0x1511 = "/usr/appl/sequence/tse3_12b195.wfc" ; dicom_0x0019:el_0x1287 = "NONE " ; dicom_0x0019:el_0x14d4 = " 256" ; dicom_0x0019:varid = "MNI DICOM variable" ; dicom_0x0019:el_0x1218 = -67b, -31b, 2b, 54b ; dicom_0x0019:el_0x1412 = "009.500702E-01" ; dicom_0x0019:el_0x1250 = " 1" ; dicom_0x0019:el_0x1452 = "005.500000E+01" ; dicom_0x0019:el_0x1283 = "NONE " ; dicom_0x0019:el_0x14b0 = 0b, 0b, 0b, 0b ; dicom_0x0019:el_0x1270 = " 1" ; dicom_0x0019:el_0x1212 = "003.979688E-43" ; dicom_0x0019:el_0x1050 = " 0" ; dicom_0x0019:el_0x14d7 = " 129" ; dicom_0x0019:el_0x1513 = "tse1-3" ; dicom_0x0019:el_0x14d9 = " 1" ; dicom_0x0019:el_0x14d1 = "000.000000E+00" ; dicom_0x0019:el_0x1416 = "001.542969E+00\\09.765625E-02" ; dicom_0x0019:el_0x1462 = "006.281846E-01" ; int dicom_0x0020 ; dicom_0x0020:el_0x4000 = "Anonymized" ; dicom_0x0020:el_0x0010 = "0 " ; dicom_0x0020:vartype = "group________" ; dicom_0x0020:el_0x000d = "1.3.12.2.1107.5.2.2.9082.20090324163029000" ; dicom_0x0020:el_0x0000 = 526 ; dicom_0x0020:el_0x0012 = " 1" ; dicom_0x0020:el_0x1041 = "-01.020065E+02" ; dicom_0x0020:el_0x0030 = "-01.245117E+02\\-1.051755E+02\\01.115978E+02" ; dicom_0x0020:el_0x1001 = " 1" ; dicom_0x0020:el_0x0013 = " 4" ; dicom_0x0020:el_0x000e = "1.3.12.2.1107.5.2.2.9082.20090324163538000002" ; dicom_0x0020:el_0x0011 = " 2" ; dicom_0x0020:el_0x0070 = "PLANAR" ; dicom_0x0020:el_0x0050 = "-01.020065E+02" ; dicom_0x0020:varid = "MNI DICOM variable" ; dicom_0x0020:el_0x0052 = "1.3.12.2.1107.5.2.2.9082.20090324163337000" ; dicom_0x0020:el_0x0032 = "-125\\-105.66192\\111.64036 " ; dicom_0x0020:el_0x0035 = "001.000000E+00\\-0.000000E+00\\-0.000000E+00\\00.000000E+00\\09.961947E-01\\-8.715570E-02" ; dicom_0x0020:el_0x0037 = "1\\-0\\-0\\0\\0.9961947\\-0.0871557" ; int dicom_0x0021 ; dicom_0x0021:el_0x1163 = "-01.020065E+02" ; dicom_0x0021:el_0x1124 = "000.000000E+00\\00.000000E+00" ; dicom_0x0021:el_0x1331 = " 0" ; dicom_0x0021:el_0x0010 = "SIEMENS MED " ; dicom_0x0021:el_0x1020 = 0b, 0b ; dicom_0x0021:el_0x1120 = "002.500000E+02\\02.500000E+02" ; dicom_0x0021:vartype = "group________" ; dicom_0x0021:el_0x1130 = "HEAD" ; dicom_0x0021:el_0x1344 = "000.000000E+00" ; dicom_0x0021:el_0x1322 = " 0" ; dicom_0x0021:el_0x1170 = "R \\AH\\HP " ; dicom_0x0021:el_0x2308 = "000.000000E+00\\00.000000E+00\\00.000000E+00" ; dicom_0x0021:el_0x2304 = "000.000000E+00\\00.000000E+00\\00.000000E+00" ; dicom_0x0021:el_0x0000 = 1512 ; dicom_0x0021:el_0x1342 = " 1" ; dicom_0x0021:el_0x2303 = "002.500000E+04" ; dicom_0x0021:el_0x2309 = "000.000000E+00" ; dicom_0x0021:el_0x1334 = " 0" ; dicom_0x0021:el_0x1182 = "MEA " ; dicom_0x0021:el_0x1341 = " 60" ; dicom_0x0021:el_0x116b = "000.000000E+00\\-9.961947E-01\\08.715570E-02" ; dicom_0x0021:el_0x2300 = "IMAG" ; dicom_0x0021:el_0x2310 = "004.095000E+03" ; dicom_0x0021:el_0x1370 = " 1" ; dicom_0x0021:el_0x1350 = 0b, 0b, 0b, 0b ; dicom_0x0021:el_0x1126 = " 0" ; dicom_0x0021:el_0x2331 = "005.500000E+01\\05.500000E+01\\05.500000E+01\\05.500000E+01\\05.500000E+01\\05.500000E+01\\05.500000E+01\\05.500000E+01\\05.500000E+01\\05.500000E+01\\05.500000E+01\\05.500000E+01\\05.500000E+01\\05.500000E+01\\05.500000E+01\\05.500000E+01" ; dicom_0x0021:el_0x2305 = "000.000000E+00\\00.000000E+00\\00.000000E+00" ; dicom_0x0021:el_0x1165 = 5b, 0b ; dicom_0x0021:el_0x1356 = "002.760000E+03" ; dicom_0x0021:el_0x2301 = " 256" ; dicom_0x0021:el_0x116a = "001.000000E+00\\00.000000E+00\\00.000000E+00" ; dicom_0x0021:el_0x1324 = " 0" ; dicom_0x0021:el_0x1160 = "000.000000E+00\\-1.886242E+01\\-1.007459E+02" ; dicom_0x0021:el_0x2307 = " 252\\ 256\\ 0" ; dicom_0x0021:el_0x0013 = "SIEMENS MR VA0 GEN " ; dicom_0x0021:el_0x1161 = "-00.000000E+00\\08.715570E-02\\09.961947E-01" ; dicom_0x0021:el_0x1171 = "L \\PF\\FA " ; dicom_0x0021:el_0x0011 = "SIEMENS CM VA0 CMS " ; dicom_0x0021:el_0x1330 = " 0" ; dicom_0x0021:el_0x2306 = " 252\\ 256\\ 0" ; dicom_0x0021:el_0x1132 = "HEAD" ; dicom_0x0021:el_0x1339 = "003.000000E+00" ; dicom_0x0021:varid = "MNI DICOM variable" ; dicom_0x0021:el_0x0023 = "SIEMENS MR VA0 RAW " ; dicom_0x0021:el_0x1340 = " 60" ; dicom_0x0021:el_0x2302 = " 256" ; dicom_0x0021:el_0x1122 = "001.000000E+00" ; dicom_0x0021:el_0x1343 = " 1" ; dicom_0x0021:el_0x134f = "INTERLEAVED " ; 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 = 184 ; dicom_0x0028:el_0x0100 = 16s ; dicom_0x0028:el_0x0102 = 11s ; dicom_0x0028:el_0x0030 = "009.765625E-01\\09.765625E-01" ; dicom_0x0028:el_0x0200 = 32736s ; dicom_0x0028:el_0x0040 = "RECT" ; dicom_0x0028:el_0x0011 = 256s ; dicom_0x0028:varid = "MNI DICOM variable" ; dicom_0x0028:el_0x0101 = 12s ; dicom_0x0028:el_0x1050 = "131\\ 131 " ; dicom_0x0028:el_0x1051 = "309\\ 309 " ; dicom_0x0028:el_0x0002 = 1s ; int dicom_0x0029 ; dicom_0x0029:el_0x1120 = "Anonymized" ; dicom_0x0029:vartype = "group________" ; dicom_0x0029:el_0x0000 = 92 ; dicom_0x0029:el_0x1110 = "STD 1 " ; dicom_0x0029:el_0x1152 = " 1" ; dicom_0x0029:el_0x0011 = "SIEMENS CM VA0 CMS " ; dicom_0x0029:varid = "MNI DICOM variable" ; int dicom_0x0051 ; dicom_0x0051:el_0x0010 = "SIEMENS CM VA0 CMS " ; dicom_0x0051:vartype = "group________" ; dicom_0x0051:el_0x0000 = 366 ; dicom_0x0051:el_0x1010 = "CDE\\F 59Y\\H-SP-CR\\IMAGE 4\\\\24-MAR-2009\\16:35\\TA 03:58\\AC 1\\\\\\CTO,, C\\VB33G\\ 252 *256 s\\tse1-3 180\\SCAN 1\\TR 2760.0\\TE 12.0/1\\\\?\\?\\SL 3.0\\SP -102.0\\Tra>Cor -5\\\\FoV 250*250\\?\\?\\TP 0\\?\\?\\?\\?\\SER 1-2\\\\01-JAN-1900\\*\\\\STU/IMA 2/4\\\\MAGNETOM EXPERT\\ABC\\16:35:39 " ; dicom_0x0051: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 = -138.5 ; dicominfo:varid = "MNI DICOM information variable" ; dicominfo:window_max = 2072.5 ; dicominfo:image_type = "DERIVED\\SECONDARY\\OTHER " ; int patient ; patient:version = "MINC Version 1.0" ; patient:full_name = "ABC" ; patient:vartype = "group________" ; patient:weight = 57. ; patient:birthdate = "SA " ; patient:position = "HFS " ; patient:identification = "ABC" ; patient:varid = "MINC standard variable" ; int study ; study:serial_no = " 9082" ; study:station_id = "Anonymized" ; study:study_id = "20090324.163029" ; study:software_version = "VB33G " ; study:version = "MINC Version 1.0" ; study:vartype = "group________" ; study:calibration_time = "153242.000000 " ; study:institution = "Anonymized" ; study:modality = "MRI__" ; study:start_date = "20090324" ; study:device_model = "MAGNETOM EXPERT " ; study:field_value = 0.9500702 ; study:referring_physician = "Anonymized" ; study:varid = "MINC standard variable" ; study:calibration_date = "20050304" ; study:manufacturer = "SIEMENS " ; study:start_time = "163029.686000 " ; // global attributes: :ident = "lorisadmin:ipmsa-loris:2020.06.17.13.06.07:29187:1" ; :minc_version = "2.4.02" ; :history = "Wed Jun 17 13:06:05 2020>>> dcm2mnc Dicom-pdw/ .\n", "" ; data: image-min = 0 ; image-max = 1991 ; xspace = 0 ; yspace = 0 ; zspace = -74.9935092017673 ; acquisition = 0 ; dicom_0x0008 = 0 ; dicom_0x0009 = 0 ; dicom_0x0010 = 0 ; dicom_0x0011 = 0 ; dicom_0x0018 = 0 ; dicom_0x0019 = 0 ; dicom_0x0020 = 0 ; dicom_0x0021 = 0 ; dicom_0x0028 = 0 ; dicom_0x0029 = 0 ; dicom_0x0051 = 0 ; dicom_groups = 0 ; dicominfo = 0 ; patient = 0 ; study = 0 ; } === The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cecile.madjar at mcin.ca Wed Jun 17 13:36:36 2020 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Wed, 17 Jun 2020 13:36:36 -0400 Subject: [Loris-dev] Issue dcm2mnc z_space=1 In-Reply-To: <61932DF2-8E8C-4797-96BB-607874AC4721@bwh.harvard.edu> References: <61932DF2-8E8C-4797-96BB-607874AC4721@bwh.harvard.edu> Message-ID: Hi Alfredo, not sure exactly why this is happening for this specific version of dcm2mnc. I am far from being an expert in dcm2mnc... However, I was lucky enough to get a more recent dcm2mnc from Bert a year ago that fixed a few issues (unfortunately not all) but maybe this version would fix the problem you are encountering? Would you mind testing that last version? Here is a link to the dcm2mnc binaries compiled for CentOS 7 and Ubuntu 16. Hopefully that would work for you. https://github.com/cmadjar/minc-tools/releases If that doesn't work, maybe you can create an issue on the minc-tools Github repository for the MINC tools developers? Here is the link to where you could post an issue: https://github.com/BIC-MNI/minc-tools/issues In the hope that helps. Best, C?cile On Wed, Jun 17, 2020 at 1:29 PM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Dear LorisDev team, > > We are facing an issue with some Dicoms (~400 Dicom studies) being > converted to minc files having only one slide (z_space=1) when importing > them in LORIS. This issue however seems to be happening in the version > 2.3.01 of dcm2mnc used by LORIS: > > === > $ dcm2mnc -version > > program: 2.3.01 built Jan 17 2018 17:39:49 > libminc: 2.4.02 > netcdf : 4.5.0 of Jan 17 2018 17:09:58 $ > HDF5 : 1.8.20 > === > > but not in version 2.0.07, which we have in a different environment: > > === > $ dcm2mnc -version > > program: 2.0.07 built Oct 31 2017 14:03:56 > libminc: 2.2.00 > netcdf : 4.2.1 of Oct 31 2017 13:59:53 $ > HDF5 : 1.8.8 > === > > I am attaching the output I get when converting a set of Dicoms for one > acquisition and also the mncheader of the created file. Do you know why > this might be happening? I can share a deidentified testing Dicom if this > helps. > > Regards, > Alfredo. > > Output dcm2mnc: > > === > $ dcm2mnc Dicom-pdw/ . > Checking file types... > File Dicom-pdw/000001.dcm appears to be DICOM (CD/Export). > Parsing 60 files > |<--------------------------------------------------->| > Sorting 60 files... Done sorting files. > Processing files, one series at a time... > INFO: Number of distinct coordinates: 60 > WARNING: Acquisition number is not informative. > WARNING: Image number is a mystery. > WARNING: Minimum image number is 4 > WARNING: Temporal position identifier is useless. > INFO: Acquisition number ranges from 1 to 1 > INFO: Image number ranges from 4 to 63 > INFO: Temporal position id ranges from -1 to -1. > -Parsing series info |<--First Slice at 0,102.006497,0.000000 > | > First Echo at 1,0.012000,0.000000 > First Time at 4,-61.117167,0.000000 > First Phase at 1,0.000000,0.000000 > First ChmSh at 1,0.000000,0.000000 > Warning: merging extra indices on Time axis: 1 5 > ->Warning: merging extra indices on Time axis: 1 6 > ->Warning: merging extra indices on Time axis: 1 7 > ->Warning: merging extra indices on Time axis: 1 8 > ->Warning: merging extra indices on Time axis: 1 9 > ->Warning: merging extra indices on Time axis: 1 10 > Warning: merging extra indices on Time axis: 1 11 > ->Warning: merging extra indices on Time axis: 1 12 > ->Warning: merging extra indices on Time axis: 1 13 > ->Warning: merging extra indices on Time axis: 1 14 > ->Warning: merging extra indices on Time axis: 1 15 > ->Warning: merging extra indices on Time axis: 1 16 > ->Warning: merging extra indices on Time axis: 1 17 > Warning: merging extra indices on Time axis: 1 18 > ->Warning: merging extra indices on Time axis: 1 19 > ->Warning: merging extra indices on Time axis: 1 20 > ->Warning: merging extra indices on Time axis: 1 21 > ->Warning: merging extra indices on Time axis: 1 22 > ->Warning: merging extra indices on Time axis: 1 23 > Warning: merging extra indices on Time axis: 1 24 > ->Warning: merging extra indices on Time axis: 1 25 > ->Warning: merging extra indices on Time axis: 1 26 > ->Warning: merging extra indices on Time axis: 1 27 > ->Warning: merging extra indices on Time axis: 1 28 > ->Warning: merging extra indices on Time axis: 1 29 > ->Warning: merging extra indices on Time axis: 1 30 > Warning: merging extra indices on Time axis: 1 31 > ->Warning: merging extra indices on Time axis: 1 32 > ->Warning: merging extra indices on Time axis: 1 33 > ->Warning: merging extra indices on Time axis: 1 34 > ->Warning: merging extra indices on Time axis: 1 35 > ->Warning: merging extra indices on Time axis: 1 36 > Warning: merging extra indices on Time axis: 1 37 > ->Warning: merging extra indices on Time axis: 1 38 > ->Warning: merging extra indices on Time axis: 1 39 > ->Warning: merging extra indices on Time axis: 1 40 > ->Warning: merging extra indices on Time axis: 1 41 > ->Warning: merging extra indices on Time axis: 1 42 > ->Warning: merging extra indices on Time axis: 1 43 > Warning: merging extra indices on Time axis: 1 44 > ->Warning: merging extra indices on Time axis: 1 45 > ->Warning: merging extra indices on Time axis: 1 46 > ->Warning: merging extra indices on Time axis: 1 47 > ->Warning: merging extra indices on Time axis: 1 48 > ->Warning: merging extra indices on Time axis: 1 49 > Warning: merging extra indices on Time axis: 1 50 > ->Warning: merging extra indices on Time axis: 1 51 > ->Warning: merging extra indices on Time axis: 1 52 > ->Warning: merging extra indices on Time axis: 1 53 > ->Warning: merging extra indices on Time axis: 1 54 > ->Warning: merging extra indices on Time axis: 1 55 > ->Warning: merging extra indices on Time axis: 1 56 > Warning: merging extra indices on Time axis: 1 57 > ->Warning: merging extra indices on Time axis: 1 58 > ->Warning: merging extra indices on Time axis: 1 59 > ->Warning: merging extra indices on Time axis: 1 60 > ->Warning: merging extra indices on Time axis: 1 61 > ->Warning: merging extra indices on Time axis: 1 62 > ->Warning: merging extra indices on Time axis: 1 63 > WARNING: Age was not numeric!! > -Creating minc file > |<--------------------------------------------------->| > Done processing files. > === > > mnc header > === > $ mincheader abc.mnc > hdf5 abc { > dimensions: > xspace = 256 ; > yspace = 256 ; > zspace = 1 ; > variables: > short image(zspace, yspace, xspace) ; > image:version = "MINC Version 1.0" ; > image:vartype = "group________" ; > image:valid_range = 0., 4095. ; > 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" ; > int xspace ; > xspace:version = "MINC Version 1.0" ; > xspace:spacetype = "native____" ; > xspace:vartype = "dimension____" ; > xspace:start = 125. ; > xspace:spacing = "regular__" ; > 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 = -0.9765625 ; > int yspace ; > yspace:version = "MINC Version 1.0" ; > yspace:spacetype = "native____" ; > yspace:vartype = "dimension____" ; > yspace:start = 114.989938629699 ; > yspace:spacing = "regular__" ; > yspace:alignment = "centre" ; > yspace:direction_cosines = 0., 0.996194701817766, > 0.0871557001590339 ; > yspace:comments = "Y increases from patient posterior to > anterior" ; > yspace:varid = "MINC standard variable" ; > yspace:length = 256 ; > yspace:step = -0.9765625 ; > double zspace ; > zspace:version = "MINC Version 1.0" ; > zspace:spacetype = "native____" ; > zspace:vartype = "dimension____" ; > zspace:start = 102.00649652328 ; > zspace:spacing = "regular__" ; > zspace:alignment = "centre" ; > zspace:direction_cosines = -0., -0.0871557001590339, > 0.996194701817766 ; > zspace:comments = "Z increases from patient inferior to > superior" ; > zspace:varid = "MINC standard variable" ; > zspace:length = 1 ; > zspace:step = 3. ; > int acquisition ; > acquisition:version = "MINC Version 1.0" ; > acquisition:scanning_sequence = "tse1-3" ; > acquisition:percent_phase_fov = 100. ; > acquisition:phase_enc_dir = "ROW " ; > acquisition:acquisition_id = "2" ; > acquisition:vartype = "group________" ; > acquisition:slice_thickness = 3. ; > acquisition:echo_number = 1. ; > acquisition:imaging_frequency = 40461870. ; > acquisition:injection_route = "" ; > acquisition:injection_minute = 0 ; > acquisition:window_width = 309. ; > acquisition:series_time = "163538.580000 " ; > acquisition:mr_acq_type = "2D" ; > acquisition:num_dyn_scans = 1. ; > acquisition:percent_sampling = 100. ; > acquisition:SAR = 0. ; > acquisition:injection_seconds = 0. ; > acquisition:series_description = "pdw " ; > acquisition:echo_train_length = 1. ; > acquisition:repetition_time = 2.76 ; > acquisition:acquisition_time = "163437.462833 " ; > acquisition:comments = "Anonymized" ; > acquisition:image_time = "163939.665000 " ; > acquisition:num_averages = 1. ; > acquisition:imaged_nucleus = "1H" ; > acquisition:flip_angle = 180. ; > acquisition:injection_day = 0 ; > acquisition:tracer = "?????" ; > acquisition:injection_hour = 0 ; > acquisition:injection_year = 0 ; > acquisition:varid = "MINC standard variable" ; > acquisition:injection_volume = 4.94065645841247e-323 ; > acquisition:injection_time = "\b" ; > acquisition:image_type = "DERIVED\\SECONDARY\\OTHER " ; > acquisition:start_time = "20090324 163029.686000 " ; > acquisition:window_center = 131. ; > acquisition:injection_month = 0 ; > acquisition:receive_coil = "CP Head " ; > acquisition:echo_time = 0.012 ; > int dicom_0x0008 ; > dicom_0x0008:el_0x0018 = > "1.3.12.2.1107.5.2.2.9082.20090324163538000002004" ; > dicom_0x0008:el_0x0090 = "Anonymized" ; > dicom_0x0008:el_0x1090 = "MAGNETOM EXPERT " ; > dicom_0x0008:el_0x0021 = "20090324" ; > dicom_0x0008:vartype = "group________" ; > dicom_0x0008:el_0x0000 = 524 ; > dicom_0x0008:el_0x1010 = "Anonymized" ; > dicom_0x0008:el_0x0030 = "163029.686000 " ; > dicom_0x0008:el_0x0031 = "163538.580000 " ; > dicom_0x0008:el_0x0020 = "20090324" ; > dicom_0x0008:el_0x103e = "pdw " ; > dicom_0x0008:el_0x0080 = "Anonymized" ; > dicom_0x0008:el_0x0022 = "20090324" ; > dicom_0x0008:el_0x0060 = "MR" ; > dicom_0x0008:el_0x0016 = "1.2.840.10008.5.1.4.1.1.4" ; > dicom_0x0008:el_0x0070 = "SIEMENS " ; > dicom_0x0008:el_0x2111 = "Lossless JPEG compression, > selection value 1, point transform 0, compression ratio 1.5987 " ; > dicom_0x0008:el_0x0050 = "Anonymized" ; > dicom_0x0008:varid = "MNI DICOM variable" ; > dicom_0x0008:el_0x0008 = "DERIVED\\SECONDARY\\OTHER " ; > dicom_0x0008:el_0x0005 = "ISO_IR 100" ; > dicom_0x0008:el_0x0023 = "20090324" ; > dicom_0x0008:el_0x0032 = "163437.462833 " ; > dicom_0x0008:el_0x0033 = "163939.665000 " ; > int dicom_0x0009 ; > dicom_0x0009:el_0x0010 = "SPI RELEASE 1 " ; > dicom_0x0009:vartype = "group________" ; > dicom_0x0009:el_0x1210 = "STANDARD" ; > dicom_0x0009:el_0x1227 = "163337.000000 " ; > dicom_0x0009:el_0x0000 = 332 ; > dicom_0x0009:el_0x1010 = "SPI VERSION 01.00 " ; > dicom_0x0009:el_0x1320 = "VC" ; > dicom_0x0009:el_0x0012 = "SIEMENS CM VA0 CMS " ; > dicom_0x0009:el_0x1041 = "MRUPNONE" ; > dicom_0x0009:el_0x1226 = "20090324" ; > dicom_0x0009:el_0x1213 = " 0" ; > dicom_0x0009:el_0x1214 = " 0" ; > dicom_0x0009:el_0x0013 = "SIEMENS CM VA0 LAB " ; > dicom_0x0009:el_0x1015 = "049S01MR012009032416400317" ; > dicom_0x0009:varid = "MNI DICOM variable" ; > dicom_0x0009:el_0x1316 = "728b43ed" ; > dicom_0x0009:el_0x1212 = 0b, 0b, 0b, 0b ; > dicom_0x0009:el_0x1040 = 0b, 0b ; > int dicom_0x0010 ; > dicom_0x0010:el_0x0010 = "ABC" ; > dicom_0x0010:vartype = "group________" ; > dicom_0x0010:el_0x0000 = 154 ; > dicom_0x0010:el_0x1010 = "Anonymized" ; > dicom_0x0010:el_0x0030 = "SA " ; > dicom_0x0010:el_0x1030 = "57" ; > dicom_0x0010:el_0x0040 = "Anonymized" ; > dicom_0x0010:el_0x0020 = "ABC" ; > dicom_0x0010:varid = "MNI DICOM variable" ; > int dicom_0x0011 ; > dicom_0x0011:el_0x0010 = "SPI RELEASE 1 " ; > dicom_0x0011:vartype = "group________" ; > dicom_0x0011:el_0x1123 = " 57" ; > dicom_0x0011:el_0x0000 = 126 ; > dicom_0x0011:el_0x1111 = "163029.686000 " ; > dicom_0x0011:el_0x1110 = "20090324" ; > dicom_0x0011:el_0x0011 = "SIEMENS CM VA0 CMS " ; > dicom_0x0011:varid = "MNI DICOM variable" ; > int dicom_0x0018 ; > dicom_0x0018:el_0x0086 = " 1" ; > dicom_0x0018:el_0x0021 = "NONE" ; > dicom_0x0018:el_0x1020 = "VB33G " ; > dicom_0x0018:el_0x0024 = "tse1-3" ; > dicom_0x0018:vartype = "group________" ; > dicom_0x0018:el_0x5100 = "HFS " ; > dicom_0x0018:el_0x1000 = " 9082" ; > dicom_0x0018:el_0x0000 = 420 ; > dicom_0x0018:el_0x0091 = "1 " ; > dicom_0x0018:el_0x0093 = "100 " ; > dicom_0x0018:el_0x0094 = "100 " ; > dicom_0x0018:el_0x0085 = "1H" ; > dicom_0x0018:el_0x0083 = "1 " ; > dicom_0x0018:el_0x1314 = "180 " ; > dicom_0x0018:el_0x0087 = "0.9500702 " ; > dicom_0x0018:el_0x1201 = "153242.000000 " ; > dicom_0x0018:el_0x0020 = "RM" ; > dicom_0x0018:el_0x0080 = "002.760000E+03" ; > dicom_0x0018:el_0x1312 = "ROW " ; > dicom_0x0018:el_0x0050 = "003.000000E+00" ; > dicom_0x0018:el_0x1310 = 0s, 256s, 252s, 0s ; > dicom_0x0018:varid = "MNI DICOM variable" ; > dicom_0x0018:el_0x1250 = "CP Head " ; > dicom_0x0018:el_0x1316 = "0 " ; > dicom_0x0018:el_0x0023 = "2D" ; > dicom_0x0018:el_0x0081 = "001.200000E+01" ; > dicom_0x0018:el_0x1200 = "20050304" ; > dicom_0x0018:el_0x0025 = "N " ; > dicom_0x0018:el_0x0088 = "0 " ; > dicom_0x0018:el_0x0084 = "004.046187E+01" ; > int dicom_0x0019 ; > dicom_0x0019:el_0x1296 = 1b, 39b, 0b, 0b, 1b, 39b, 0b, 0b, > 2b, 0b, 0b, 0b ; > dicom_0x0019:el_0x14d6 = " 0" ; > dicom_0x0019:el_0x14a6 = > "001.000000E+02\\04.348140E+00\\04.422564E+00" ; > dicom_0x0019:el_0x1455 = "001.022977E+02" ; > dicom_0x0019:el_0x1482 = "002.000000E+02" ; > dicom_0x0019:el_0x1285 = "NONE " ; > dicom_0x0019:el_0x14a2 = "001.034203E+00" ; > dicom_0x0019:el_0x1245 = " 1" ; > dicom_0x0019:el_0x1422 = "002.700000E+01" ; > dicom_0x0019:el_0x0010 = "SIEMENS CM VA0 CMS " ; > dicom_0x0019:el_0x1020 = "EXAMNONE" ; > dicom_0x0019:vartype = "group________" ; > dicom_0x0019:el_0x14a0 = " 1" ; > dicom_0x0019:el_0x1211 = "002.388881E+02" ; > dicom_0x0019:el_0x1294 = "001.570796E+00" ; > dicom_0x0019:el_0x1471 = "004.698000E+00" ; > dicom_0x0019:el_0x14d3 = "001.000000E+00" ; > dicom_0x0019:el_0x1060 = "131072" ; > dicom_0x0019:el_0x1297 = 64b, 8b, -64b, 1b, -22b, -76b, > -1b, -1b ; > dicom_0x0019:el_0x1210 = "002.388881E+02" ; > dicom_0x0019:el_0x1472 = "008.000000E+00" ; > dicom_0x0019:el_0x0000 = 1900 ; > dicom_0x0019:el_0x1231 = " 256" ; > dicom_0x0019:el_0x14da = "PLUSX " ; > dicom_0x0019:el_0x1228 = " -126" ; > dicom_0x0019:el_0x0015 = "SIEMENS CM VA0 ACQU" ; > dicom_0x0019:el_0x1010 = " 50" ; > dicom_0x0019:el_0x14d2 = "NONE" ; > dicom_0x0019:el_0x0012 = "SIEMENS MR VA0 GEN " ; > dicom_0x0019:el_0x1451 = "005.500000E+01" ; > dicom_0x0019:el_0x14a5 = > "001.500000E+00\\05.203557E-02\\00.000000E+00" ; > dicom_0x0019:el_0x1230 = " 256" ; > dicom_0x0019:el_0x0014 = "SIEMENS MR VA0 COAD" ; > dicom_0x0019:el_0x1226 = " 125" ; > dicom_0x0019:el_0x1512 = "SIEMENS " ; > dicom_0x0019:el_0x1421 = " 2" ; > dicom_0x0019:el_0x1030 = "A IRS " ; > dicom_0x0019:el_0x1414 = "001.000000E+01" ; > dicom_0x0019:el_0x1213 = "002.000000E+01" ; > dicom_0x0019:el_0x1260 = "001.800000E+02" ; > dicom_0x0019:el_0x1298 = > "000.000000E+00\\00.000000E+00\\00.000000E+00" ; > dicom_0x0019:el_0x14d5 = " 0" ; > dicom_0x0019:el_0x1456 = " 25000" ; > dicom_0x0019:el_0x1454 = "-01.000000E+00" ; > dicom_0x0019:el_0x1240 = " 0" ; > dicom_0x0019:el_0x1460 = "006.025031E-01" ; > dicom_0x0019:el_0x1420 = "001.660000E+02" ; > dicom_0x0019:el_0x1470 = "004.698000E+00" ; > dicom_0x0019:el_0x1424 = "003.908454E+01" ; > dicom_0x0019:el_0x1510 = > "/usr/appl/proto/014/c/head/LAQ302/PDW_AX.prg" ; > dicom_0x0019:el_0x1290 = " 0" ; > dicom_0x0019:el_0x1480 = > "001.430000E+02\\01.570000E+02\\01.450000E+02" ; > dicom_0x0019:el_0x1221 = " 252" ; > dicom_0x0019:el_0x1450 = "008.900000E+01" ; > dicom_0x0019:el_0x1220 = " 252" ; > dicom_0x0019:el_0x1426 = "006.584084E+01" ; > dicom_0x0019:el_0x1214 = " 1" ; > dicom_0x0019:el_0x14d8 = " 129" ; > dicom_0x0019:el_0x1216 = 1b, 1b, 69b, 0b, 64b, 0b, 0b, 0b ; > dicom_0x0019:el_0x1281 = "NONE " ; > dicom_0x0019:el_0x1511 = > "/usr/appl/sequence/tse3_12b195.wfc" ; > dicom_0x0019:el_0x1287 = "NONE " ; > dicom_0x0019:el_0x14d4 = " 256" ; > dicom_0x0019:varid = "MNI DICOM variable" ; > dicom_0x0019:el_0x1218 = -67b, -31b, 2b, 54b ; > dicom_0x0019:el_0x1412 = "009.500702E-01" ; > dicom_0x0019:el_0x1250 = " 1" ; > dicom_0x0019:el_0x1452 = "005.500000E+01" ; > dicom_0x0019:el_0x1283 = "NONE " ; > dicom_0x0019:el_0x14b0 = 0b, 0b, 0b, 0b ; > dicom_0x0019:el_0x1270 = " 1" ; > dicom_0x0019:el_0x1212 = "003.979688E-43" ; > dicom_0x0019:el_0x1050 = " 0" ; > dicom_0x0019:el_0x14d7 = " 129" ; > dicom_0x0019:el_0x1513 = "tse1-3" ; > dicom_0x0019:el_0x14d9 = " 1" ; > dicom_0x0019:el_0x14d1 = "000.000000E+00" ; > dicom_0x0019:el_0x1416 = "001.542969E+00\\09.765625E-02" ; > dicom_0x0019:el_0x1462 = "006.281846E-01" ; > int dicom_0x0020 ; > dicom_0x0020:el_0x4000 = "Anonymized" ; > dicom_0x0020:el_0x0010 = "0 " ; > dicom_0x0020:vartype = "group________" ; > dicom_0x0020:el_0x000d = > "1.3.12.2.1107.5.2.2.9082.20090324163029000" ; > dicom_0x0020:el_0x0000 = 526 ; > dicom_0x0020:el_0x0012 = " 1" ; > dicom_0x0020:el_0x1041 = "-01.020065E+02" ; > dicom_0x0020:el_0x0030 = > "-01.245117E+02\\-1.051755E+02\\01.115978E+02" ; > dicom_0x0020:el_0x1001 = " 1" ; > dicom_0x0020:el_0x0013 = " 4" ; > dicom_0x0020:el_0x000e = > "1.3.12.2.1107.5.2.2.9082.20090324163538000002" ; > dicom_0x0020:el_0x0011 = " 2" ; > dicom_0x0020:el_0x0070 = "PLANAR" ; > dicom_0x0020:el_0x0050 = "-01.020065E+02" ; > dicom_0x0020:varid = "MNI DICOM variable" ; > dicom_0x0020:el_0x0052 = > "1.3.12.2.1107.5.2.2.9082.20090324163337000" ; > dicom_0x0020:el_0x0032 = "-125\\-105.66192\\111.64036 " ; > dicom_0x0020:el_0x0035 = > "001.000000E+00\\-0.000000E+00\\-0.000000E+00\\00.000000E+00\\09.961947E-01\\-8.715570E-02" > ; > dicom_0x0020:el_0x0037 = > "1\\-0\\-0\\0\\0.9961947\\-0.0871557" ; > int dicom_0x0021 ; > dicom_0x0021:el_0x1163 = "-01.020065E+02" ; > dicom_0x0021:el_0x1124 = "000.000000E+00\\00.000000E+00" ; > dicom_0x0021:el_0x1331 = " 0" ; > dicom_0x0021:el_0x0010 = "SIEMENS MED " ; > dicom_0x0021:el_0x1020 = 0b, 0b ; > dicom_0x0021:el_0x1120 = "002.500000E+02\\02.500000E+02" ; > dicom_0x0021:vartype = "group________" ; > dicom_0x0021:el_0x1130 = "HEAD" ; > dicom_0x0021:el_0x1344 = "000.000000E+00" ; > dicom_0x0021:el_0x1322 = " 0" ; > dicom_0x0021:el_0x1170 = "R \\AH\\HP " ; > dicom_0x0021:el_0x2308 = > "000.000000E+00\\00.000000E+00\\00.000000E+00" ; > dicom_0x0021:el_0x2304 = > "000.000000E+00\\00.000000E+00\\00.000000E+00" ; > dicom_0x0021:el_0x0000 = 1512 ; > dicom_0x0021:el_0x1342 = " 1" ; > dicom_0x0021:el_0x2303 = "002.500000E+04" ; > dicom_0x0021:el_0x2309 = "000.000000E+00" ; > dicom_0x0021:el_0x1334 = " 0" ; > dicom_0x0021:el_0x1182 = "MEA " ; > dicom_0x0021:el_0x1341 = " 60" ; > dicom_0x0021:el_0x116b = > "000.000000E+00\\-9.961947E-01\\08.715570E-02" ; > dicom_0x0021:el_0x2300 = "IMAG" ; > dicom_0x0021:el_0x2310 = "004.095000E+03" ; > dicom_0x0021:el_0x1370 = " 1" ; > dicom_0x0021:el_0x1350 = 0b, 0b, 0b, 0b ; > dicom_0x0021:el_0x1126 = " 0" ; > dicom_0x0021:el_0x2331 = > "005.500000E+01\\05.500000E+01\\05.500000E+01\\05.500000E+01\\05.500000E+01\\05.500000E+01\\05.500000E+01\\05.500000E+01\\05.500000E+01\\05.500000E+01\\05.500000E+01\\05.500000E+01\\05.500000E+01\\05.500000E+01\\05.500000E+01\\05.500000E+01" > ; > dicom_0x0021:el_0x2305 = > "000.000000E+00\\00.000000E+00\\00.000000E+00" ; > dicom_0x0021:el_0x1165 = 5b, 0b ; > dicom_0x0021:el_0x1356 = "002.760000E+03" ; > dicom_0x0021:el_0x2301 = " 256" ; > dicom_0x0021:el_0x116a = > "001.000000E+00\\00.000000E+00\\00.000000E+00" ; > dicom_0x0021:el_0x1324 = " 0" ; > dicom_0x0021:el_0x1160 = > "000.000000E+00\\-1.886242E+01\\-1.007459E+02" ; > dicom_0x0021:el_0x2307 = " 252\\ 256\\ 0" ; > dicom_0x0021:el_0x0013 = "SIEMENS MR VA0 GEN " ; > dicom_0x0021:el_0x1161 = > "-00.000000E+00\\08.715570E-02\\09.961947E-01" ; > dicom_0x0021:el_0x1171 = "L \\PF\\FA " ; > dicom_0x0021:el_0x0011 = "SIEMENS CM VA0 CMS " ; > dicom_0x0021:el_0x1330 = " 0" ; > dicom_0x0021:el_0x2306 = " 252\\ 256\\ 0" ; > dicom_0x0021:el_0x1132 = "HEAD" ; > dicom_0x0021:el_0x1339 = "003.000000E+00" ; > dicom_0x0021:varid = "MNI DICOM variable" ; > dicom_0x0021:el_0x0023 = "SIEMENS MR VA0 RAW " ; > dicom_0x0021:el_0x1340 = " 60" ; > dicom_0x0021:el_0x2302 = " 256" ; > dicom_0x0021:el_0x1122 = "001.000000E+00" ; > dicom_0x0021:el_0x1343 = " 1" ; > dicom_0x0021:el_0x134f = "INTERLEAVED " ; > 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 = 184 ; > dicom_0x0028:el_0x0100 = 16s ; > dicom_0x0028:el_0x0102 = 11s ; > dicom_0x0028:el_0x0030 = "009.765625E-01\\09.765625E-01" ; > dicom_0x0028:el_0x0200 = 32736s ; > dicom_0x0028:el_0x0040 = "RECT" ; > dicom_0x0028:el_0x0011 = 256s ; > dicom_0x0028:varid = "MNI DICOM variable" ; > dicom_0x0028:el_0x0101 = 12s ; > dicom_0x0028:el_0x1050 = "131\\ 131 " ; > dicom_0x0028:el_0x1051 = "309\\ 309 " ; > dicom_0x0028:el_0x0002 = 1s ; > int dicom_0x0029 ; > dicom_0x0029:el_0x1120 = "Anonymized" ; > dicom_0x0029:vartype = "group________" ; > dicom_0x0029:el_0x0000 = 92 ; > dicom_0x0029:el_0x1110 = "STD 1 " ; > dicom_0x0029:el_0x1152 = " 1" ; > dicom_0x0029:el_0x0011 = "SIEMENS CM VA0 CMS " ; > dicom_0x0029:varid = "MNI DICOM variable" ; > int dicom_0x0051 ; > dicom_0x0051:el_0x0010 = "SIEMENS CM VA0 CMS " ; > dicom_0x0051:vartype = "group________" ; > dicom_0x0051:el_0x0000 = 366 ; > dicom_0x0051:el_0x1010 = "CDE\\F 59Y\\H-SP-CR\\IMAGE > 4\\\\24-MAR-2009\\16:35\\TA 03:58\\AC 1\\\\\\CTO,, C\\VB33G\\ 252 > *256 s\\tse1-3 180\\SCAN 1\\TR 2760.0\\TE 12.0/1\\\\?\\?\\SL > 3.0\\SP -102.0\\Tra>Cor -5\\\\FoV 250*250\\?\\?\\TP > 0\\?\\?\\?\\?\\SER 1-2\\\\01-JAN-1900\\*\\\\STU/IMA 2/4\\\\MAGNETOM > EXPERT\\ABC\\16:35:39 " ; > dicom_0x0051: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 = -138.5 ; > dicominfo:varid = "MNI DICOM information variable" ; > dicominfo:window_max = 2072.5 ; > dicominfo:image_type = "DERIVED\\SECONDARY\\OTHER " ; > int patient ; > patient:version = "MINC Version 1.0" ; > patient:full_name = "ABC" ; > patient:vartype = "group________" ; > patient:weight = 57. ; > patient:birthdate = "SA " ; > patient:position = "HFS " ; > patient:identification = "ABC" ; > patient:varid = "MINC standard variable" ; > int study ; > study:serial_no = " 9082" ; > study:station_id = "Anonymized" ; > study:study_id = "20090324.163029" ; > study:software_version = "VB33G " ; > study:version = "MINC Version 1.0" ; > study:vartype = "group________" ; > study:calibration_time = "153242.000000 " ; > study:institution = "Anonymized" ; > study:modality = "MRI__" ; > study:start_date = "20090324" ; > study:device_model = "MAGNETOM EXPERT " ; > study:field_value = 0.9500702 ; > study:referring_physician = "Anonymized" ; > study:varid = "MINC standard variable" ; > study:calibration_date = "20050304" ; > study:manufacturer = "SIEMENS " ; > study:start_time = "163029.686000 " ; > > // global attributes: > :ident = > "lorisadmin:ipmsa-loris:2020.06.17.13.06.07:29187:1" ; > :minc_version = "2.4.02" ; > :history = "Wed Jun 17 13:06:05 2020>>> dcm2mnc Dicom-pdw/ > .\n", > "" ; > data: > > image-min = 0 ; > > image-max = 1991 ; > > xspace = 0 ; > > yspace = 0 ; > > zspace = -74.9935092017673 ; > > acquisition = 0 ; > > dicom_0x0008 = 0 ; > > dicom_0x0009 = 0 ; > > dicom_0x0010 = 0 ; > > dicom_0x0011 = 0 ; > > dicom_0x0018 = 0 ; > > dicom_0x0019 = 0 ; > > dicom_0x0020 = 0 ; > > dicom_0x0021 = 0 ; > > dicom_0x0028 = 0 ; > > dicom_0x0029 = 0 ; > > dicom_0x0051 = 0 ; > > dicom_groups = 0 ; > > dicominfo = 0 ; > > patient = 0 ; > > study = 0 ; > } > === > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: