[MINC-users] MINC -> Analyze conversion problem
christophe grova
minc-users@bic.mni.mcgill.ca
Wed, 28 May 2003 22:19:01 -0600
Hello everybody,
My name is Christophe Grova and I am a new post doc arrived at the MNI in
Jean Gotman's team (EEG department). I try tu use 'mnc2ana' to convert a
MINC file in an analyze file.
I obtained really strange results in my analyze header ! Especially, my
dimensions are completely false !
For info, here is a dump of my analyze header followed by a dump of the
header of the MINC
file (using mincheader : this header seems ok )
Using the Display software I have no problem to look at this MINC file on my
PC under linux ... !
Do you have any idea? Thanks a lot in advance ,
Best regards,
Christophe
***************************
Christophe Grova, PhD
PostDoc - EEG department
Montreal Neurological Institute, McGill University
3801 University Street, Montreal, Quebec, Canada, H3A 2B4
email : christophe.grova@mail.mcgill.ca
tel : (514) 398 2184
fax : (514) 398 8106
***************************
ANALYZE HEADER:
-------------------------------
Analyze Header Dump of: <C***_20010724_1_2_mri.hdr>
sizeof_hdr: <348>
data_type: <0>
db_name: <>
extents: <16384>
session_error: <0>
regular: <r>
hkey_un0: <0>
dim[0]: <4>
dim[1]: <-21822>
dim[2]: <0>
dim[3]: <1>
dim[4]: <1>
dim[5]: <0>
dim[6]: <0>
dim[7]: <0>
vox_units: <>
cal_units: <>
unused1: <0>
datatype: <1024>
bitpix: <4096>
pixdim[0]: <-32.0000>
pixdim[1]: <0.0000>
pixdim[2]: <0.0000>
pixdim[3]: <1.0059>
pixdim[4]: <-0.0000>
pixdim[5]: <0.0000>
pixdim[6]: <0.0000>
pixdim[7]: <0.0000>
vox_offset: <%6.4>
funused1: <0.0000>
funused2: <-32.0000>
funused3: <0.0000>
cal_max: <0.0000>
cal_min: <0.0000>
compressed: <0>
verified: <0>
glmax: <0>
glmin: <-1077739520>
descrip: <ΓΏ>
aux_file: <>
orient: <0>
originator: <>
generated: <>
scannum: <>
patient_id: <>
exp_date: <>
exp_time: <>
hist_un0: <>
views: <0>
vols_added: <0>
start_field:<0>
field_skip: <0>
omax: <0>
omin: <0>
smax: <0>
smin: <0>
Header of the corresponding MINC file using mincheader :
netcdf mincheader-12520-tmp {
dimensions:
xspace = 170 ;
zspace = 256 ;
yspace = 256 ;
variables:
double xspace(xspace) ;
xspace:varid = "MINC standard variable" ;
xspace:vartype = "dimension____" ;
xspace:version = "MINC Version 1.0" ;
xspace:comments = "X increases from patient left to right" ;
xspace:spacing = "regular__" ;
xspace:alignment = "centre" ;
xspace:step = -0.999999999999999 ;
xspace:start = 62.6907997131348 ;
xspace:spacetype = "native____" ;
xspace:direction_cosines = 1., -0., 0. ;
int zspace ;
zspace:varid = "MINC standard variable" ;
zspace:vartype = "dimension____" ;
zspace:version = "MINC Version 1.0" ;
zspace:comments = "Z increases from patient inferior to superior" ;
zspace:spacing = "regular__" ;
zspace:alignment = "centre" ;
zspace:step = -1. ;
zspace:start = 115.464775085449 ;
zspace:spacetype = "native____" ;
zspace:direction_cosines = 0., -0., 1. ;
int yspace ;
yspace:varid = "MINC standard variable" ;
yspace:vartype = "dimension____" ;
yspace:version = "MINC Version 1.0" ;
yspace:comments = "Y increases from patient posterior to anterior" ;
yspace:spacing = "regular__" ;
yspace:alignment = "centre" ;
yspace:step = -1. ;
yspace:start = 139.535224914551 ;
yspace:spacetype = "native____" ;
yspace:direction_cosines = 0., 1., 0. ;
short image(xspace, zspace, yspace) ;
image:parent = "rootvariable" ;
image:varid = "MINC standard variable" ;
image:vartype = "group________" ;
image:version = "MINC Version 1.0" ;
image:signtype = "signed__" ;
image:valid_range = 0., 4095. ;
image:complete = "true_" ;
image:image-min = "--->image-min" ;
image:image-max = "--->image-max" ;
int rootvariable ;
rootvariable:varid = "MINC standard variable" ;
rootvariable:vartype = "group________" ;
rootvariable:version = "MINC Version 1.0" ;
rootvariable:parent = "" ;
rootvariable:children = "image\n",
"patient\n",
"study\n",
"acquisition\n",
"dicominfo\n",
"dicom_groups" ;
double image-min(xspace) ;
image-min:varid = "MINC standard variable" ;
image-min:vartype = "var_attribute" ;
image-min:version = "MINC Version 1.0" ;
image-min:_FillValue = 0. ;
image-min:parent = "image" ;
double image-max(xspace) ;
image-max:varid = "MINC standard variable" ;
image-max:vartype = "var_attribute" ;
image-max:version = "MINC Version 1.0" ;
image-max:_FillValue = 1. ;
image-max:parent = "image" ;
int patient ;
patient:parent = "rootvariable" ;
patient:varid = "MINC standard variable" ;
patient:vartype = "group________" ;
patient:version = "MINC Version 1.0" ;
patient:full_name = "c***, r*** " ;
patient:identification = "1519860 " ;
patient:birthdate = "19810616" ;
patient:sex = "male__" ;
patient:weight = 90. ;
int study ;
study:parent = "rootvariable" ;
study:varid = "MINC standard variable" ;
study:vartype = "group________" ;
study:version = "MINC Version 1.0" ;
study:start_time = "20010724 104029.201" ;
study:modality = "MRI__" ;
study:institution = "Montreal Neuro Institute" ;
study:station_id = "mrc " ;
study:study_id = "20010724" ;
study:acquisition_id = "1_2" ;
int acquisition ;
acquisition:parent = "rootvariable" ;
acquisition:varid = "MINC standard variable" ;
acquisition:vartype = "group________" ;
acquisition:version = "MINC Version 1.0" ;
acquisition:scanning_sequence = "fl3d_ns_11b65_vali" ;
acquisition:repetition_time = 0.025 ;
acquisition:echo_time = 0.011 ;
acquisition:flip_angle = 30. ;
acquisition:num_averages = 1. ;
acquisition:imaging_frequency = 63604645. ;
acquisition:imaged_nucleus = "1H" ;
int dicominfo ;
dicominfo:vartype = "group________" ;
dicominfo:varid = "MNI DICOM information variable" ;
dicominfo:parent = "rootvariable" ;
dicominfo:window_min = -18. ;
dicominfo:window_max = 416.5 ;
dicominfo:xspace-indices = 6269, 6169, 6069, 5969, 5869, 5769, 5669,
5569, 5469, 5369, 5269, 5169, 5069, 4969, 4869, 4769, 4669, 4569, 4469,
4369, 4269, 4169, 4069, 3969, 3869, 3769, 3669, 3569, 3469, 3369, 3269,
3169, 3069, 2969, 2869, 2769, 2669, 2569, 2469, 2369, 2269, 2169, 2069,
1969, 1869, 1769, 1669, 1569, 1469, 1369, 1269, 1169, 1069, 969, 869, 769,
669, 569, 469, 369, 269, 169,
69, -31, -131, -231, -331, -431, -531, -631, -731, -831, -931, -1031, -1131,
-1231, -1331, -1431, -1531, -1631, -1731, -1831, -1931, -2031, -2131, -2231
, -2331, -2431, -2531, -2631, -2731, -2831, -2931, -3031, -3131, -3231, -333
1, -3431, -3531, -3631, -3731, -3831, -3931, -4031, -4131, -4231, -4331, -44
31, -4531, -4631, -4731, -4831, -4931, -5031, -5131, -5231, -5331, -5431, -5
531, -5631, -5731, -5831, -5931, -6031, -6131, -6231, -6331, -6431, -6531, -
6631, -6731, -6831, -6931, -7031, -7131, -7231, -7331, -7431, -7531, -7631,
-7731, -7831, -7931, -8031, -8131, -8231, -8331, -8431, -8531, -8631, -8731,
-8831, -8931, -9031, -9131, -9231, -9331, -9431, -9531, -9631, -9731, -9831
, -9931, -10031, -10131, -10231, -10331, -10431, -10531, -10631 ;
int dicom_groups ;
dicom_groups:vartype = "group________" ;
dicom_groups:varid = "MNI DICOM variable" ;
dicom_groups:parent = "rootvariable" ;
dicom_groups:children = "dicom_0x0008\n",
"dicom_0x0009\n",
"dicom_0x0010\n",
"dicom_0x0011\n",
"dicom_0x0018\n",
"dicom_0x0019\n",
"dicom_0x0020\n",
"dicom_0x0021\n",
"dicom_0x0028\n",
"dicom_0x0029" ;
int dicom_0x0008 ;
dicom_0x0008:vartype = "group________" ;
dicom_0x0008:varid = "MNI DICOM variable" ;
dicom_0x0008:parent = "dicom_groups" ;
dicom_0x0008:el_0x0000 = 0b, 0b, 1b, 82b ;
dicom_0x0008:el_0x0008 = "ORIGINAL\\PRIMARY\\UNDEFINED" ;
dicom_0x0008:el_0x0016 = 49b, 46b, 50b, 46b, 56b, 52b, 48b, 46b,
49b, 48b, 48b, 48b, 56b, 46b, 53b, 46b, 49b, 46b, 52b, 46b, 49b, 46b, 49b,
46b, 52b, 0b ;
dicom_0x0008:el_0x0018 = 49b, 46b, 55b, 51b, 46b, 56b, 48b, 46b,
49b, 49b, 52b, 46b, 53b, 56b, 46b, 57b, 55b, 46b, 49b, 48b, 46b, 56b, 48b,
54b, 52b, 46b, 50b, 48b, 48b, 49b, 48b, 55b, 50b, 52b, 49b, 50b, 49b, 52b,
49b, 49b, 46b, 48b, 48b, 48b, 48b, 48b, 48b, 49b, 50b, 0b ;
dicom_0x0008:el_0x0020 = "20010724" ;
dicom_0x0008:el_0x0022 = "20010724" ;
dicom_0x0008:el_0x0023 = "20010724" ;
dicom_0x0008:el_0x0030 = "104029.201" ;
dicom_0x0008:el_0x0032 = "104030.210" ;
dicom_0x0008:el_0x0033 = "105625.000" ;
dicom_0x0008:el_0x0060 = "MR" ;
dicom_0x0008:el_0x0070 = "SIEMENS " ;
dicom_0x0008:el_0x0080 = "Montreal Neuro Institute" ;
dicom_0x0008:el_0x0090 = "" ;
dicom_0x0008:el_0x1010 = "mrc " ;
dicom_0x0008:el_0x1080 = "" ;
dicom_0x0008:el_0x1090 = "MAGNETOM VISION " ;
int dicom_0x0009 ;
dicom_0x0009:vartype = "group________" ;
dicom_0x0009:varid = "MNI DICOM variable" ;
dicom_0x0009:parent = "dicom_groups" ;
dicom_0x0009:el_0x0000 = 0b, 0b, 0b, 66b ;
dicom_0x0009:el_0x1226 = "20010724" ;
dicom_0x0009:el_0x1227 = "103354.000" ;
dicom_0x0009:el_0x1316 = "723a610a" ;
dicom_0x0009:el_0x1320 = "VC " ;
int dicom_0x0010 ;
dicom_0x0010:vartype = "group________" ;
dicom_0x0010:varid = "MNI DICOM variable" ;
dicom_0x0010:parent = "dicom_groups" ;
dicom_0x0010:el_0x0000 = 0b, 0b, 0b, 90b ;
dicom_0x0010:el_0x0010 = "c***, r*** " ;
dicom_0x0010:el_0x0020 = "1519860 " ;
dicom_0x0010:el_0x0030 = "19810616" ;
dicom_0x0010:el_0x0040 = "M " ;
dicom_0x0010:el_0x1010 = "020Y" ;
dicom_0x0010:el_0x1030 = "90" ;
int dicom_0x0011 ;
dicom_0x0011:vartype = "group________" ;
dicom_0x0011:varid = "MNI DICOM variable" ;
dicom_0x0011:parent = "dicom_groups" ;
dicom_0x0011:el_0x0000 = 0b, 0b, 0b, 44b ;
dicom_0x0011:el_0x1110 = "20010724" ;
dicom_0x0011:el_0x1111 = "103343.000" ;
dicom_0x0011:el_0x1123 = "90" ;
int dicom_0x0018 ;
dicom_0x0018:vartype = "group________" ;
dicom_0x0018:varid = "MNI DICOM variable" ;
dicom_0x0018:parent = "dicom_groups" ;
dicom_0x0018:el_0x0000 = 0b, 0b, 0b, -40b ;
dicom_0x0018:el_0x0021 = "NONE\\NONE " ;
dicom_0x0018:el_0x0050 = "1 " ;
dicom_0x0018:el_0x0080 = "25" ;
dicom_0x0018:el_0x0081 = "11" ;
dicom_0x0018:el_0x0083 = "1 " ;
dicom_0x0018:el_0x0084 = "63.604645 " ;
dicom_0x0018:el_0x0085 = "1H" ;
dicom_0x0018:el_0x0086 = "1 " ;
dicom_0x0018:el_0x0090 = "256 " ;
dicom_0x0018:el_0x1000 = " 7321" ;
dicom_0x0018:el_0x1020 = "VB33A " ;
dicom_0x0018:el_0x1200 = "20010704" ;
dicom_0x0018:el_0x1201 = "112159.000" ;
dicom_0x0018:el_0x1250 = "CP Head " ;
dicom_0x0018:el_0x1314 = "30" ;
int dicom_0x0019 ;
dicom_0x0019:vartype = "group________" ;
dicom_0x0019:varid = "MNI DICOM variable" ;
dicom_0x0019:parent = "dicom_groups" ;
dicom_0x0019:el_0x0000 = 0b, 0b, 3b, 72b ;
dicom_0x0019:el_0x1010 = "60" ;
dicom_0x0019:el_0x1050 = "0 " ;
dicom_0x0019:el_0x1060 = "131072" ;
dicom_0x0019:el_0x1210 = "954.5383644104" ;
dicom_0x0019:el_0x1211 = "954.5383644104" ;
dicom_0x0019:el_0x1212 = "3.97968763868248e-43" ;
dicom_0x0019:el_0x1213 = "60" ;
dicom_0x0019:el_0x1214 = "1 " ;
dicom_0x0019:el_0x1220 = "224 " ;
dicom_0x0019:el_0x1221 = "224 " ;
dicom_0x0019:el_0x1226 = "111 " ;
dicom_0x0019:el_0x1228 = "-112" ;
dicom_0x0019:el_0x1230 = "256 " ;
dicom_0x0019:el_0x1231 = "256 " ;
dicom_0x0019:el_0x1250 = "1 " ;
dicom_0x0019:el_0x1260 = "30" ;
dicom_0x0019:el_0x1270 = "40" ;
dicom_0x0019:el_0x1290 = "0 " ;
dicom_0x0019:el_0x1294 = "0 " ;
dicom_0x0019:el_0x1298 = "0\\0\\0 " ;
dicom_0x0019:el_0x1412 = "1.49380624294281" ;
dicom_0x0019:el_0x1414 = "10" ;
dicom_0x0019:el_0x1416 = "8.2578125 " ;
dicom_0x0019:el_0x1420 = "220 " ;
dicom_0x0019:el_0x1421 = "1 " ;
dicom_0x0019:el_0x1422 = "34" ;
dicom_0x0019:el_0x1424 = "74.7226943969727" ;
dicom_0x0019:el_0x1426 = "92.5243682861328" ;
dicom_0x0019:el_0x1450 = "88.3300018310547" ;
dicom_0x0019:el_0x1451 = "64.8600006103516" ;
dicom_0x0019:el_0x1452 = "53.4700012207031" ;
dicom_0x0019:el_0x1454 = "-1" ;
dicom_0x0019:el_0x1455 = "101.62767791748 " ;
dicom_0x0019:el_0x1456 = "8500" ;
dicom_0x0019:el_0x1460 = "0.0149458236992359" ;
dicom_0x0019:el_0x1462 = "0.595520436763763 " ;
dicom_0x0019:el_0x1470 = "1.529296875 " ;
dicom_0x0019:el_0x1471 = "1.529296875 " ;
dicom_0x0019:el_0x1472 = "0.705882370471954 " ;
dicom_0x0019:el_0x1482 = "200 " ;
dicom_0x0019:el_0x1490 = "" ;
dicom_0x0019:el_0x14a0 = "1 " ;
dicom_0x0019:el_0x14a2 = "1.18286526203156" ;
dicom_0x0019:el_0x14b0 = "0 " ;
dicom_0x0019:el_0x1510 =
"/usr/appl/proto/016/c/head/Head_coil_fMRI/global_t1W.prg" ;
dicom_0x0019:el_0x1511 =
"/usr/vali/pargen/anatomical/fl3d_ns_11b65_vali.wkc" ;
dicom_0x0019:el_0x1512 = "USER" ;
dicom_0x0019:el_0x1513 = "fl3d" ;
int dicom_0x0020 ;
dicom_0x0020:vartype = "group________" ;
dicom_0x0020:varid = "MNI DICOM variable" ;
dicom_0x0020:parent = "dicom_groups" ;
dicom_0x0020:el_0x0000 = 0b, 0b, 1b, 60b ;
dicom_0x0020:el_0x000d = 49b, 46b, 55b, 51b, 46b, 56b, 48b, 46b,
49b, 49b, 52b, 46b, 53b, 56b, 46b, 57b, 55b, 46b, 49b, 48b, 46b, 56b, 48b,
54b, 52b, 46b, 50b, 48b, 48b, 49b, 48b, 55b, 50b, 52b, 49b, 50b, 49b, 52b,
49b, 49b, 46b, 48b, 48b, 48b, 48b, 48b, 48b, 49b, 51b, 0b ;
dicom_0x0020:el_0x000e = 49b, 46b, 55b, 51b, 46b, 56b, 48b, 46b,
49b, 49b, 52b, 46b, 53b, 56b, 46b, 57b, 55b, 46b, 49b, 48b, 46b, 56b, 48b,
54b, 52b, 46b, 50b, 48b, 48b, 49b, 48b, 55b, 50b, 52b, 49b, 50b, 49b, 52b,
49b, 49b, 46b, 48b, 48b, 48b, 48b, 48b, 48b, 49b, 52b, 0b ;
dicom_0x0020:el_0x0010 = "2 " ;
dicom_0x0020:el_0x0011 = "1 " ;
dicom_0x0020:el_0x0012 = "1 " ;
dicom_0x0020:el_0x0013 = "4 " ;
dicom_0x0020:el_0x0032 =
"-62.6907997131348\\-139.535224914551\\115.464775085449" ;
dicom_0x0020:el_0x0037 = "0\\1\\-0\\0\\-0\\-1" ;
dicom_0x0020:el_0x0050 = "0 " ;
dicom_0x0020:el_0x0052 = 49b, 46b, 55b, 51b, 46b, 56b, 48b, 46b,
49b, 49b, 52b, 46b, 53b, 56b, 46b, 57b, 55b, 46b, 49b, 48b, 46b, 56b, 48b,
54b, 52b, 46b, 50b, 48b, 48b, 49b, 48b, 55b, 50b, 52b, 49b, 50b, 49b, 52b,
49b, 49b, 46b, 48b, 48b, 48b, 48b, 48b, 48b, 49b, 53b, 0b ;
dicom_0x0020:el_0x1001 = "1 " ;
int dicom_0x0021 ;
dicom_0x0021:vartype = "group________" ;
dicom_0x0021:varid = "MNI DICOM variable" ;
dicom_0x0021:parent = "dicom_groups" ;
dicom_0x0021:el_0x0000 = 0b, 0b, 1b, 88b ;
dicom_0x0021:el_0x1020 = 0b, 0b ;
dicom_0x0021:el_0x1122 = "1 " ;
dicom_0x0021:el_0x1160 =
"-62.6907997131348\\12.0352249145508\\12.0352249145508 " ;
dicom_0x0021:el_0x1161 = "1\\0\\-0" ;
dicom_0x0021:el_0x1163 = "-62.6907997131348 " ;
dicom_0x0021:el_0x1165 = 1b, 0b ;
dicom_0x0021:el_0x116a = "0\\-1\\0" ;
dicom_0x0021:el_0x116b = "0\\0\\1 " ;
dicom_0x0021:el_0x1180 = "Head_coil_fMRI/global_t1W " ;
dicom_0x0021:el_0x1322 = "0 " ;
dicom_0x0021:el_0x1324 = "0 " ;
dicom_0x0021:el_0x1330 = "170 " ;
dicom_0x0021:el_0x1331 = "170 " ;
dicom_0x0021:el_0x1334 = "170 " ;
dicom_0x0021:el_0x1336 = "1 " ;
dicom_0x0021:el_0x1339 = "170 " ;
dicom_0x0021:el_0x1340 = "1 " ;
dicom_0x0021:el_0x1341 = "1 " ;
dicom_0x0021:el_0x1342 = "1 " ;
dicom_0x0021:el_0x1343 = "1 " ;
dicom_0x0021:el_0x1344 = "-19222" ;
dicom_0x0021:el_0x1356 = "25" ;
dicom_0x0021:el_0x1370 = "1 " ;
int dicom_0x0028 ;
dicom_0x0028:vartype = "group________" ;
dicom_0x0028:varid = "MNI DICOM variable" ;
dicom_0x0028:parent = "dicom_groups" ;
dicom_0x0028:el_0x0000 = 0b, 0b, 0b, -86b ;
dicom_0x0028:el_0x0002 = 1b, 0b ;
dicom_0x0028:el_0x0004 = "MONOCHROME2 " ;
dicom_0x0028:el_0x0005 = 2b, 0b ;
dicom_0x0028:el_0x0010 = 0b, 1b ;
dicom_0x0028:el_0x0011 = 0b, 1b ;
dicom_0x0028:el_0x0030 = "1\\1 " ;
dicom_0x0028:el_0x0100 = 16b, 0b ;
dicom_0x0028:el_0x0101 = 12b, 0b ;
dicom_0x0028:el_0x0102 = 11b, 0b ;
dicom_0x0028:el_0x0103 = 0b, 0b ;
dicom_0x0028:el_0x0200 = -32b, 127b ;
dicom_0x0028:el_0x1050 = "41\\41 " ;
dicom_0x0028:el_0x1051 = "96\\96 " ;
dicom_0x0028:el_0x1052 = "0 " ;
dicom_0x0028:el_0x1053 = "1 " ;
int dicom_0x0029 ;
dicom_0x0029:vartype = "group________" ;
dicom_0x0029:varid = "MNI DICOM variable" ;
dicom_0x0029:parent = "dicom_groups" ;
dicom_0x0029:el_0x0000 = 0b, 0b, 0b, 10b ;
dicom_0x0029:el_0x1152 = "1 " ;
// global attributes:
:history = "Tue Jul 24 12:09:26 2001>>> dicomserver\n",
"" ;
}