[MINC-users] mincreeample transformation problem
Colin Shaun Hawco, M
colin.hawco at mail.mcgill.ca
Wed Apr 3 12:40:37 EDT 2013
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!
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