[MINC-users] processing rootvariable in mincheader

Mon Mar 7 22:00:27 EST 2016

Hi Mishkin,

The processing variable you speak of to my knowledge is only written
by minctracc, I wasn't aware that it read this data back in. Perhaps
it's using this as a starting transformation.

I haven't ever seen this behaviour but should track this down. To be
clear you get different results with minctracc dependent on if a MINC
volume has these header fields defined?

a

On 8 March 2016 at 12:20, Mishkin Derakhshan <mishkind at gmail.com> wrote:
> 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
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