[MINC-users] processing rootvariable in mincheader

Mon Mar 7 21:20:06 EST 2016

Hi,
Can anyone provide some insight about the processing rootvariable in
the mincheader. It contains attributes like
processing:transformation0-filename
processing:transformation0-filedata
processing:transformation1-inverted

I'm finding that I get different results from minctracc depending on
if a file has a transformation listed in here or not.

Below is an example header. If I use mincedit and remove the
processing rootvariable and all it's attributes altogether I get
_different_ results. I'm still trying to figure out which is the
_right_ answer. Might have to do with my version of minctracc too.

thanks,
mishkin

$ mincheader *nonbrain.mnc.gz
netcdf mincheader-21838-tmp {
dimensions:
zspace = 60 ;
yspace = 256 ;
xspace = 256 ;
variables:
int rootvariable ;
rootvariable:varid = "MINC standard variable" ;
rootvariable:vartype = "group________" ;
rootvariable:version = "MINC Version    1.0" ;
rootvariable:parent = "" ;
rootvariable:children = "image\n",
"processing" ;
int processing ;
processing:parent = "rootvariable" ;
processing:transformation0-filename =
"/tmp/TMP.2016-03-07.06:15:58.mishkin.nbcr.pl.8848/MOCK2_NBCRSym_CFG1_001_w48_t1p_ISPC-stx152lsq6total.xfm"
;
processing:transformation0-filedata = "MNI Transform File\n",
"%Mon Mar  7 06:17:48 2016>>> /usr/local/mni/bin/minctracc
/tmp/1371178.1.nrx2.short.q/mritotal_9798//MOCK2_NBCRSym_CFG1_001_w48_t1p_ISPC-stx152lsq6_8_dxyz.mnc
/trials/quarantine/common/models/icbm_avg_152_t1_tal_lin_symmetric_8_dxyz.mnc
/tmp/TMP.2016-03-07.06:15:58.mishkin.nbcr.pl.8848/MOCK2_NBCRSym_CFG1_001_w48_t1p_ISPC-stx152lsq6total.xfm
-transformation
/tmp/1371178.1.nrx2.short.q/mritotal_9798//MOCK2_NBCRSym_CFG1_001_w48_t1p_ISPC-stx152lsq6_8tmp2c.xfm
-lsq9 -xcorr -model_mask
/trials/quarantine/common/models/icbm_avg_152_t1_tal_lin_symmetric_8_mask.mnc
-center 0.016856 -21.055166 -3.738050 -step 4 4 4 -tol 0.004 -simplex
2\n",
"%(Package mni_autoreg 0.99.2, compiled by rotor at romeo
(i686-pc-linux-gnu) on Mon May  8 23:16:34 EDT 2006)\n",
"\n",
"Transform_Type = Linear;\n",
"Linear_Transform =\n",
" 1.17811584472656 0.00353206926956773 -0.0036923938896507 0.387569785118103\n",
" -0.00324956281110644 1.08965194225311 0.00551541242748499 2.76728820800781\n",
" 0.00381157570518553 -0.00611468823626637 1.21029341220856
2.98504638671875;\n",
"" ;
processing:transformation1-filename =
"/tmp/TMP.2016-03-07.06:15:58.mishkin.nbcr.pl.8848/MOCK2_NBCRSym_CFG1_001_w48_t1p_ISPC-stx152lsq6total.xfm"
;
processing:transformation1-filedata = "MNI Transform File\n",
"%Mon Mar  7 06:17:48 2016>>> /usr/local/mni/bin/minctracc
/tmp/1371178.1.nrx2.short.q/mritotal_9798//MOCK2_NBCRSym_CFG1_001_w48_t1p_ISPC-stx152lsq6_8_dxyz.mnc
/trials/quarantine/common/models/icbm_avg_152_t1_tal_lin_symmetric_8_dxyz.mnc
/tmp/TMP.2016-03-07.06:15:58.mishkin.nbcr.pl.8848/MOCK2_NBCRSym_CFG1_001_w48_t1p_ISPC-stx152lsq6total.xfm
-transformation
/tmp/1371178.1.nrx2.short.q/mritotal_9798//MOCK2_NBCRSym_CFG1_001_w48_t1p_ISPC-stx152lsq6_8tmp2c.xfm
-lsq9 -xcorr -model_mask
/trials/quarantine/common/models/icbm_avg_152_t1_tal_lin_symmetric_8_mask.mnc
-center 0.016856 -21.055166 -3.738050 -step 4 4 4 -tol 0.004 -simplex
2\n",
"%(Package mni_autoreg 0.99.2, compiled by rotor at romeo
(i686-pc-linux-gnu) on Mon May  8 23:16:34 EDT 2006)\n",
"\n",
"Transform_Type = Linear;\n",
"Linear_Transform =\n",
" 1.17811584472656 0.00353206926956773 -0.0036923938896507 0.387569785118103\n",
" -0.00324956281110644 1.08965194225311 0.00551541242748499 2.76728820800781\n",
" 0.00381157570518553 -0.00611468823626637 1.21029341220856
2.98504638671875;\n",
"" ;
processing:transformation1-inverted = "true_" ;
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 = 3. ;
zspace:start = -72. ;
zspace:direction_cosines = 0., 0., 1. ;
zspace:units = "mm" ;
zspace:spacetype = "talairach_" ;
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 = -126. ;
yspace:direction_cosines = 0., 1., 0. ;
yspace:units = "mm" ;
yspace:spacetype = "talairach_" ;
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 = 1. ;
xspace:start = -90. ;
xspace:direction_cosines = 1., 0., 0. ;
xspace:units = "mm" ;
xspace:spacetype = "talairach_" ;
double image-max(zspace) ;
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(zspace) ;
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" ;
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:complete = "true_" ;
image:signtype = "unsigned" ;
image:valid_range = 0., 65535. ;

// global attributes:
:history = "Mon Mar  7 06:17:29 2016>>> minccalc -clobber -expression
A[0]<=0.1 && A[0]>=-0.1 ? A[1]:0
/tmp/TMP.2016-03-07.06:15:58.mishkin.nbcr.pl.8848/dilated_brain.mask.mnc
/tmp/TMP.2016-03-07.06:15:58.mishkin.nbcr.pl.8848/MOCK2_NBCRSym_CFG1_001_w48_t1p_ISPC-stx152lsq6.mnc.gz
/tmp/TMP.2016-03-07.06:15:58.mishkin.nbcr.pl.8848/nonbrain_native.mnc\n",
"Mon Mar  7 06:17:50 2016>>> mincresample -clobber -like
/trials/quarantine/common/models/icbm_avg_152_t1_tal_lin_symmetric.mnc
-transformation
/tmp/TMP.2016-03-07.06:15:58.mishkin.nbcr.pl.8848/MOCK2_NBCRSym_CFG1_001_w48_t1p_ISPC-stx152lsq6total.xfm
/tmp/TMP.2016-03-07.06:15:58.mishkin.nbcr.pl.8848/nonbrain_native.mnc
/tmp/TMP.2016-03-07.06:15:58.mishkin.nbcr.pl.8848/nonbrain_stx.mnc\n",
"Mon Mar  7 06:17:51 2016>>> mincreshape -clobber -dimrange
zspace=48,103 /tmp/TMP.2016-03-07.06:15:58.mishkin.nbcr.pl.8848/nonbrain_stx.mnc
/tmp/TMP.2016-03-07.06:15:58.mishkin.nbcr.pl.8848/nonbrain_stx_cropped.mnc\n",
"Mon Mar  7 06:17:51 2016>>> mincresample -clobber -like
/tmp/TMP.2016-03-07.06:15:58.mishkin.nbcr.pl.8848/MOCK2_NBCRSym_CFG1_001_w48_t1p_ISPC-stx152lsq6.mnc.gz
/tmp/TMP.2016-03-07.06:15:58.mishkin.nbcr.pl.8848/nonbrain_stx_cropped.mnc
/tmp/TMP.2016-03-07.06:15:58.mi