[MINC-users] mincreeample transformation problem
Colin Shaun Hawco, M
colin.hawco at mail.mcgill.ca
Wed Apr 3 12:38:41 EDT 2013
Thanks for the replies,
The attached file just showed an axial slice of EPI, with the data shirted forward such that the front of the brain is cut off by the edge of the image.
OK, here are the mincheaders (this will be a bit of a long message):
T1 image
netcdf p121_anat {
dimensions:
xspace = 160 ;
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 = 1. ;
xspace:start = -74.777108669281 ;
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 = 125.30120491982 ;
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 = 167.1325302124 ;
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 = "pt121" ;
patient:identification = "09.03.27-10:18:12-DST-1.3.12.2.1107.5.2.14.16505" ;
patient:birthdate = "19830703" ;
patient:age = "025Y" ;
patient:sex = "female" ;
patient:weight = 57. ;
int study ;
study:parent = "rootvariable" ;
study:varid = "MINC standard variable" ;
study:vartype = "group________" ;
study:version = "MINC Version 1.0" ;
study:start_date = "20090327" ;
study:start_time = "101814.640000 " ;
study:modality = "MRI__" ;
study:manufacturer = "SIEMENS " ;
study:model = "SonataVision" ;
study:field_value = 1.5 ;
study:software_version = "syngo MR A30 4VA30A " ;
study:serial_no = "16505 " ;
study:calibration_date = "20050630" ;
study:institution = "McConnell Brain Imaging Center" ;
study:station_id = "MRC " ;
study:performing_physician = "" ;
study:operator = "lm" ;
study:procedure = "FUNCTIONAL^Dr Lepage" ;
study:study_id = "20090328.101814" ;
int acquisition ;
acquisition:parent = "rootvariable" ;
acquisition:varid = "MINC standard variable" ;
acquisition:vartype = "group________" ;
acquisition:version = "MINC Version 1.0" ;
acquisition:acquisition_id = "4" ;
acquisition:start_time = "20090327 101814.640000 " ;
acquisition:scanning_sequence = "*fl3d1_ns " ;
acquisition:protocol_name = "GLOBAL_no angulation" ;
acquisition:receive_coil = "CP_HeadArray" ;
acquisition:transmit_coil = "Body" ;
acquisition:repetition_time = 0.022 ;
acquisition:echo_time = 0.0092 ;
acquisition:echo_number = 0. ;
acquisition:flip_angle = 30. ;
acquisition:slice_thickness = 1. ;
acquisition:num_slices = 1. ;
acquisition:num_dyn_scans = 1. ;
acquisition:num_averages = 1. ;
acquisition:imaging_frequency = 63687939. ;
acquisition:imaged_nucleus = "1H" ;
acquisition:window_center = 46. ;
acquisition:window_width = 135. ;
acquisition:num_phase_enc_steps = 256. ;
acquisition:percent_sampling = 10000. ;
acquisition:percent_phase_fov = 10000. ;
acquisition:pixel_bandwidth = 70. ;
acquisition:phase_enc_dir = "ROW" ;
acquisition:SAR = 0.03627666831017 ;
acquisition:mr_acq_type = "3D" ;
acquisition:image_type = "ORIGINAL\\PRIMARY\\M\\ND " ;
acquisition:MrProt_dump = "disabled" ;
int dicominfo ;
dicominfo:vartype = "group________" ;
dicominfo:varid = "MNI DICOM information variable" ;
dicominfo:parent = "rootvariable" ;
dicominfo:window_min = -34. ;
dicominfo:window_max = 467.5 ;
int dicom_groups ;
dicom_groups:vartype = "group________" ;
dicom_groups:varid = "MNI DICOM variable" ;
dicom_groups:parent = "rootvariable" ;
dicom_groups:children = "dicom_0x0008\n",
"dicom_0x0010\n",
"dicom_0x0018\n",
"dicom_0x0019\n",
"dicom_0x0020\n",
"dicom_0x0021\n",
"dicom_0x0023\n",
"dicom_0x0028\n",
"dicom_0x0029\n",
"dicom_0x0032\n",
"dicom_0x0040\n",
"dicom_0x0051\n",
"dicom_0x7fe0" ;
int dicom_0x0008 ;
dicom_0x0008:vartype = "group________" ;
dicom_0x0008:varid = "MNI DICOM variable" ;
dicom_0x0008:parent = "dicom_groups" ;
dicom_0x0008:el_0x0000 = 0b, 0b, 3b, 112b ;
dicom_0x0008:el_0x0005 = "ISO_IR 100" ;
dicom_0x0008:el_0x0008 = "ORIGINAL\\PRIMARY\\M\\ND " ;
dicom_0x0008:el_0x0016 = "1.2.840.10008.5.1.4.1.1.4" ;
dicom_0x0008:el_0x0018 = "1.3.12.2.1107.5.2.14.16505.30000009032714261626500000429" ;
dicom_0x0008:el_0x0020 = "20090327" ;
dicom_0x0008:el_0x0021 = "20090327" ;
dicom_0x0008:el_0x0022 = "20090327" ;
dicom_0x0008:el_0x0023 = "20090327" ;
dicom_0x0008:el_0x0030 = "101814.640000 " ;
dicom_0x0008:el_0x0031 = "110250.203000 " ;
dicom_0x0008:el_0x0032 = "104737.934998 " ;
dicom_0x0008:el_0x0033 = "110252.171000 " ;
dicom_0x0008:el_0x0050 = "" ;
dicom_0x0008:el_0x0060 = "MR" ;
dicom_0x0008:el_0x0070 = "SIEMENS " ;
dicom_0x0008:el_0x0080 = "McConnell Brain Imaging Center" ;
dicom_0x0008:el_0x0081 = "3801University, Montreal /5032D1/, Quebec, H3A2B4, CA " ;
dicom_0x0008:el_0x0090 = "" ;
dicom_0x0008:el_0x1010 = "MRC " ;
dicom_0x0008:el_0x1030 = "FUNCTIONAL^Dr Lepage" ;
dicom_0x0008:el_0x103e = "GLOBAL_no angulation" ;
dicom_0x0008:el_0x1050 = "RESEARCH" ;
dicom_0x0008:el_0x1070 = "lm" ;
dicom_0x0008:el_0x1090 = "SonataVision" ;
And an example EPI Image
netcdf epi_file {
dimensions:
zspace = 30 ;
yspace = 64 ;
xspace = 64 ;
variables:
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 = 5.00000023980207 ;
zspace:units = "mm" ;
zspace:start = -69.2670692002613 ;
zspace:direction_cosines = 0.0886361496853597, -0.0451411970661573, 0.995040655097262 ;
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 = 3.99999998616676 ;
yspace:units = "mm" ;
yspace:start = -114.419242845404 ;
yspace:direction_cosines = -0.0666440429608072, 0.996465269196971, 0.0511423388402057 ;
int 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 = -3.9999998858578 ;
xspace:units = "mm" ;
xspace:start = 137.159234295035 ;
xspace:direction_cosines = 0.993832080113542, 0.070846596891737, -0.0853144550826576 ;
double image-max ;
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" ;
double image-min ;
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" ;
int study ;
study:parent = "rootvariable" ;
study:varid = "MINC standard variable" ;
study:vartype = "group________" ;
study:version = "MINC Version 1.0" ;
int rootvariable ;
rootvariable:varid = "MINC standard variable" ;
rootvariable:vartype = "group________" ;
rootvariable:version = "MINC Version 1.0" ;
rootvariable:parent = "" ;
rootvariable:children = "study\n",
"patient\n",
"acquisition\n",
"image" ;
int patient ;
patient:parent = "rootvariable" ;
patient:varid = "MINC standard variable" ;
patient:vartype = "group________" ;
patient:version = "MINC Version 1.0" ;
patient:full_name = "3T 2D EP TR=3000ms/TE=30ms/FA=90deg 24-Jul-2012 11:33:1.78 Mosaic" ;
int acquisition ;
acquisition:parent = "rootvariable" ;
acquisition:varid = "MINC standard variable" ;
acquisition:vartype = "group________" ;
acquisition:version = "MINC Version 1.0" ;
short image(zspace, yspace, xspace) ;
image:parent = "rootvariable" ;
image:varid = "MINC standard variable" ;
image:vartype = "group________" ;
image:version = "MINC Version 1.0" ;
image:image-max = "--->image-max" ;
image:image-min = "--->image-min" ;
image:signtype = "signed__" ;
image:valid_range = 0., 2049. ;
// global attributes:
:ident = "chawc:node17:2013.03.05.09.52.34:17491:1" ;
:minc_version = "2.1.01" ;
:history = "Tue Mar 5 09:52:34 2013>>> nii2mnc -quiet tf240720121100-113301-00033-00033-1.hdr /imaging/scratch/Daskalakis/chawc/Data/minc/p121/run1/tf240720121100-113301-00033-00033-1.mnc\n",
"" ;
data:
zspace = _ ;
yspace = _ ;
xspace = _ ;
image-max = 2049 ;
image-min = 0 ;
study = _ ;
rootvariable = _ ;
patient = _ ;
acquisition = _ ;
}
And just to be complete, the EPI Template image to which I want to resample the EPI data
netcdf EPI_template {
dimensions:
zspace = 91 ;
yspace = 109 ;
xspace = 91 ;
variables:
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 = 2. ;
zspace:units = "mm" ;
zspace:start = -72. ;
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 = 2. ;
yspace:units = "mm" ;
yspace:start = -126. ;
yspace:direction_cosines = 0., 1., 0. ;
int 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 = -2. ;
xspace:units = "mm" ;
xspace:start = 90. ;
xspace:direction_cosines = 1., -0., -0. ;
double image-max ;
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" ;
double image-min ;
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" ;
int study ;
study:parent = "rootvariable" ;
study:varid = "MINC standard variable" ;
study:vartype = "group________" ;
study:version = "MINC Version 1.0" ;
int rootvariable ;
rootvariable:varid = "MINC standard variable" ;
rootvariable:vartype = "group________" ;
rootvariable:version = "MINC Version 1.0" ;
rootvariable:parent = "" ;
rootvariable:children = "study\n",
"patient\n",
"acquisition\n",
"image" ;
int patient ;
patient:parent = "rootvariable" ;
patient:varid = "MINC standard variable" ;
patient:vartype = "group________" ;
patient:version = "MINC Version 1.0" ;
patient:full_name = "NIFTI-1 Image" ;
int acquisition ;
acquisition:parent = "rootvariable" ;
acquisition:varid = "MINC standard variable" ;
acquisition:vartype = "group________" ;
acquisition:version = "MINC Version 1.0" ;
byte image(zspace, yspace, xspace) ;
image:parent = "rootvariable" ;
image:varid = "MINC standard variable" ;
image:vartype = "group________" ;
image:version = "MINC Version 1.0" ;
image:image-max = "--->image-max" ;
image:image-min = "--->image-min" ;
image:signtype = "unsigned" ;
image:valid_range = 0., 255. ;
// global attributes:
:ident = "colin:penfield:2012.11.05.14.08.29:27799:1" ;
:minc_version = "2.1.01" ;
:history = "Mon Nov 5 14:08:29 2012>>> nii2mnc /projects/colin/work/spm8/templates/EPI.nii /projects/colin/EPI_template.mnc\n",
"" ;
data:
zspace = _ ;
yspace = _ ;
xspace = _ ;
image-max = 0.831372529501095 ;
image-min = 0 ;
study = _ ;
rootvariable = _ ;
patient = _ ;
acquisition = _ ;
}
I very much appreciate the help!
Colin Hawco, PhD
Post Doctoral Researcher
Temerty Centre for Therapeutic Brain Intervention
Centre for Addiction and Mental Health (CAMH)
University of Toronto
"Disorder Expands"
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