[MINC-users] processing rootvariable in mincheader
Mishkin Derakhshan
mishkind at gmail.com
Tue Mar 8 16:59:19 EST 2016
Hi Andrew,
I've been trying to simplify the problem down to its most basic
reproducible form and in doing so it looks like the problem isn't with
minctracc, but somewhere else in my pipeline. If I can get something
reproducible I will post it.
mishkin
On Mon, Mar 7, 2016 at 5:00 PM, Andrew Janke <a.janke at gmail.com> wrote:
> 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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