[MINC-users] mincaverage error
Lisa F. Akiyama
lrisa87 at uw.edu
Mon Mar 7 14:04:05 EST 2011
Alex Z.,
Here's a list of pre-processing I performed on each site S and site I files
before putting them through mincaverage:
1) N3 intensity nonuniformity correction
2) mincnorm so that the range would be 0-100
3) Linear registration of subject images to standard template: bestlinreg
using Vladimir Fonov's NIHPD-BIC model for 00-02 year age range (range
0-100) as the target. I also created a brain mask image and specified as the
target_mask that in the command. Used -lsq9.
When I look at the header of the files, they all have a stamp mentioning
that the files went through mincresample with -like NIHPD-BIC template.
I've check each individual's resampled image and they all seem fairly
well registered. (There were a few images that didn't do so well, but after
creating the subject specific brainmask and re-running bestlinreg on these
individuals, the outcomes were good)
I just ran mincinfo on all files: They all have the same dimension lengths,
steps and start values.
I'm not sure whether I should run the following as you suggested earlier
since I've registered them to a standard template already and also because
they have the same dimensions.
If you do want to register them without prior registration, you could
> still get this to work by simply resampling all volumes to one of
> them, e.g.,
> mincresample -like <file1.mnc> <file2.mnc> <file2_resampled.mnc>
Claude,
mincinfo and mincheader will give you information about the orientation
of the images. Watch for +ve vs -ve steps, voxel sizes, start coords,
direction cosines, storage format.
It seems like all files have very similar headers. Regardless of which site
the scan came from, they had the same dimension length, step, start,
direction cosine, and units (mm) for x, y, and z.
I've attached mincinfo and mincheader outputs for S1 and I1 to this email
for your reference.
For example, S1+S2+...+SN+S1+S2+... Does adding more images make
it blow up? I want you to repeat images of the same site, not mixed
sites.
I ran the following trials:
1) mincaverage -normalize -filelist all-S-site-files.txt Savg.mnc ===> OK;
looks fine
2) mincaverage -normalize -filelist all-I-site-files.txt Iavg.mnc ===> OK;
looks fine
3) mincaverage -normalize -filelist Savg.mnc-and-all-S-site-files.txt ===>
ERROR; miicv_attach: MINC package entry point
ncvarid: ncid -1: NetCDF: Not a valid ID
3a) mincaverage -normalize -filelist Savg.mnc-and-one-S-site-file.txt ===>
OK.
3b) mincaverage -normalize -filelist Savg.mnc-and-27(out of 28
total)-S-site_files.txt ===> OK. Same size, looks identical to original
Savg.mnc
However, when I ran Savg.mnc-and-27-S-site-files (removed a different
subject image than previously), error message "
ncvarid: ncid -1: NetCDF: Not a valid ID" appeared. Haven't tested
for all possible pairings.
4) mincaverage -normalize -filelist Iavg.mnc-and-all-I-site-files.txt ===>
OK; looks fine, same size and looks identical to original Iavg.mnc
4a) mincaverage -normalize -filelist Iavg.mnc-and-14(out of 15
total)-I-site-files.txt (tried this with removing different subjects each
time although I haven't tested all possible pairings) ===> OK; looks good,
same size, and looks identical to original Iavg.mnc
It appears that there is something sketchy with the site S files rather than
the site I files.
Thank you.
Best,
Lisa
On Sat, Mar 5, 2011 at 8:45 PM, Claude LEPAGE <claude at bic.mni.mcgill.ca>wrote:
> Hi,
>
> I thought about the resampling issue too, as suggested by Alex,
> but after doing a mincaverage -help:
>
> -check_dimensions: Check that dimension info matches across files
> (default).
> -nocheck_dimensions: Do not check dimension info.
>
> It seems that the default is to check dimensions! Maybe the check
> is wrong...
>
> Lisa, since you don't get an error when averaging images from the
> same site, can you keep adding more images from the same site?
> For example, S1+S2+...+SN+S1+S2+... Does adding more images make
> it blow up? I want you to repeat images of the same site, not mixed
> sites.
>
> mincinfo and mincheader will give you information about the orientation
> of the images. Watch for +ve vs -ve steps, voxel sizes, start coords,
> direction cosines, storage format. Alex's suggestion to resample
> like a template file makes a lot of sense.
>
> When you manage to obtain an output, does it make sense when you
> look at it in register/Display?
>
> Claude
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
-------------- next part --------------
#################3mincinfo I1 (SEA0092)##########3
image: signed__ float 0 to 100
image dimensions: xspace yspace zspace
dimension name length step start
-------------- ------ ---- -----
xspace 195 1 -96
yspace 233 1 -134
zspace 159 1 -72
#############33mincheader I1###############
dimensions:
xspace = 195 ;
yspace = 233 ;
zspace = 159 ;
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 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 = -96. ;
xspace:direction_cosines = 1., 0., 0. ;
xspace:units = "mm" ;
xspace:spacetype = "native____" ;
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 = -134. ;
yspace:direction_cosines = 0., 1., 0. ;
yspace:units = "mm" ;
yspace:spacetype = "native____" ;
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 = -72. ;
zspace:direction_cosines = 0., 0., 1. ;
zspace:units = "mm" ;
zspace:spacetype = "native____" ;
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" ;
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" ;
int processing ;
processing:parent = "rootvariable" ;
processing:transformation0-filename = "SEA0092_6mo_May2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg.xfm" ;
processing:transformation0-filedata = "MNI Transform File\n",
"%Wed Mar 2 17:21:31 2011>>> minctracc -clobber -xcorr -lsq9 -step 4 4 4 -simplex 2 -tol 0.004 -transformation /tmp/bestlinreg.pl-sl6JOF_9/SSEA0092_6mo_May2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm_3.xfm -model_mask ../nihpd_asym_00-02_t1w_brainmask.mnc /tmp/bestlinreg.pl-sl6JOF_9/SSEA0092_6mo_May2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm_4_dxyz.mnc /tmp/bestlinreg.pl-sl6JOF_9/Tnihpd_asym_00-02_t1w_4_dxyz.mnc /tmp/bestlinreg.pl-sl6JOF_9/SSEA0092_6mo_May2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm_4.xfm\n",
"%(Package mni_autoreg 0.99.6, compiled by @harold (x86_64-unknown-linux-gnu) on Thu Jan 20 17:08:53 EST 2011)\n",
"\n",
"Transform_Type = Linear;\n",
"Linear_Transform =\n",
" 0.886912822723389 0.269598573446274 0.0238081403076649 -2.6237313747406\n",
" -0.293741941452026 0.990325748920441 -0.271627128124237 -3.88510131835938\n",
" -0.0957735255360603 0.231416314840317 0.947292149066925 -33.9751396179199;\n",
"" ;
float image(xspace, yspace, zspace) ;
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:valid_range = 0.f, 100.f ;
image:signtype = "signed__" ;
// global attributes:
:ident = "todd:neptune-ubuntu:2011.03.02.17.21.34:2157:1" ;
:history = "/usr/local/bic/bin/nu_correct SEA0092_6mo_May2009_t1mpr_flipped-MNI152maskedout.mnc SEA0092_6mo_May2009_t1mpr_flipped-MNI152maskedout_nu.mnc\n",
"Fri Feb 25 17:12:07 2011>>> minccalc -clobber -expression ((A[0] < 0.136172323) ? 0.0 : (A[0] > 401.7866021) ? 1.0 : (A[0]-0.136172323)/401.650429777) * 100 + 0; SEA0092_6mo_May2009_t1mpr_flipped-MNI152maskedout_nu.mnc SEA0092_6mo_May2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm.mnc\n",
"Wed Mar 2 17:21:34 2011>>> mincresample -clobber -like ../nihpd_asym_00-02_t1w.mnc -transformation SEA0092_6mo_May2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg.xfm SEA0092_6mo_May2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm.mnc SEA0092_6mo_May2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg.mnc\n",
"" ;
data:
rootvariable = _ ;
xspace = 0 ;
yspace = 0 ;
zspace = 0 ;
image-max = 1.17549435082229e-36, 1.17549435082229e-36,
1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36,
1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36,
1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36,
1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36,
1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36,
1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36,
1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36,
1.17549435082229e-36, 0.947396136382664, 2.42943418526572,
3.54712807798542, 5.43007380506798, 5.24310234752484, 5.34829036556262,
6.67209047055415, 10.9288733599668, 36.3487172599864, 84.8257225260093,
86.2320458650952, 90.3107790048268, 92.2324197538925, 94.4303746139242,
96.9602554939775, 96.8229717281455, 99.4185221494169, 99.3028232343371,
95.476047313064, 98.4255065946472, 96.6541113780925, 96.2440155508314,
95.325919366911, 97.5437208419121, 98.8889750341048, 99.6204374013019,
98.7399874243647, 97.4958232829498, 99.3923948702791, 99.7868374144113,
97.8121961832795, 96.5177085762091, 96.7953910055525, 98.6316597357256,
97.9282868455072, 98.0283044621664, 97.1196919634517, 98.5740097319334,
97.2217874433856, 96.2067240535846, 96.6066800776357, 96.9111508415941,
97.722676894639, 95.8158241034866, 96.6164974642248, 95.842644229338,
97.8234382249037, 95.142019165114, 98.7558462433008, 96.8567822834201,
94.4411746711171, 95.5269437288598, 94.4053363201693, 95.2683228963663,
96.8755942915174, 94.5648617855763, 95.2961733007075, 94.6672412578908,
95.5333153334278, 95.5588387998097, 95.7181933978884, 95.291576669733,
93.9703407365886, 97.6117804010904, 97.8813425222601, 92.8648519011405,
96.7612560713554, 98.7097134523909, 95.0144032274814, 97.8932007660336,
97.1219070847972, 93.9673501663108, 98.570064369599, 98.6346160250637,
97.6427544638386, 96.5268292662264, 96.1117424933994, 95.7841816373158,
95.4984849750389, 99.8054726310361, 98.9702733679704, 97.3082051035661,
96.8274130793568, 98.5531583853512, 98.0989370432797, 98.6487713857531,
99.365122813149, 98.7167349832031, 97.0260366549247, 97.5701973996575,
96.4080303281864, 97.2090986210998, 95.7935528188491, 98.8743078605843,
95.8149198309595, 94.3582954014065, 96.1299116322933, 97.5014546825681,
98.1822037203252, 96.4361661001698, 96.1891188778678, 98.2764253443323,
98.6383014165164, 98.3532371837748, 97.9850191314124, 95.7594893304802,
95.5377338007302, 97.4838081314802, 98.4664580900451, 99.6746324150443,
98.36076392894, 98.8901044035188, 98.4092890653164, 99.5249301842105,
99.99660375537, 99.7408373777891, 99.3233241861749, 99.5521028959736,
98.7816594609443, 98.9743221160359, 98.7226090870193, 100,
98.7184866641343, 97.5502477986922, 91.6209743283614, 96.7875721928541,
89.8002411071914, 89.4762705750763, 90.745842506823, 85.6993147347808,
90.3850492926194, 88.401299455667, 90.0115786773621, 85.0384803163856,
82.9575836413033, 65.5508104448483, 40.7643453389398, 15.3182288875258,
8.25609948865467, 7.55357639700481, 5.20630582965026, 3.4388455204862,
2.92469247968065, 2.06481643009108, 1.72675695938155, 0.0296052310782467,
1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36,
1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36,
1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36,
1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36,
1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36,
1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36,
1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36,
1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36,
1.17549435082229e-36 ;
image-min = 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0 ;
processing = 0 ;
}
-------------- next part --------------
###########3mincinfo S1 (15331)###############
image: signed__ float 0 to 99.98685455322265625
image dimensions: xspace yspace zspace
dimension name length step start
-------------- ------ ---- -----
xspace 195 1 -96
yspace 233 1 -134
zspace 159 1 -72
##############3mincheader S1###################
dimensions:
xspace = 195 ;
yspace = 233 ;
zspace = 159 ;
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 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 = -96. ;
xspace:direction_cosines = 1., 0., 0. ;
xspace:units = "mm" ;
xspace:spacetype = "native____" ;
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 = -134. ;
yspace:direction_cosines = 0., 1., 0. ;
yspace:units = "mm" ;
yspace:spacetype = "native____" ;
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 = -72. ;
zspace:direction_cosines = 0., 0., 1. ;
zspace:units = "mm" ;
zspace:spacetype = "native____" ;
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" ;
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" ;
int processing ;
processing:parent = "rootvariable" ;
processing:transformation0-filename = "15331_001_MNI152maskedout_RAS_nu_mincnorm-reg_nihpd_bestlinreg.xfm" ;
processing:transformation0-filedata = "MNI Transform File\n",
"%Wed Mar 2 16:49:19 2011>>> minctracc -clobber -xcorr -lsq9 -step 4 4 4 -simplex 2 -tol 0.004 -transformation /tmp/bestlinreg.pl-fGFwUogf/S15331_001_MNI152maskedout_RAS_nu_mincnorm_3.xfm -model_mask ../nihpd_asym_00-02_t1w_brainmask.mnc /tmp/bestlinreg.pl-fGFwUogf/S15331_001_MNI152maskedout_RAS_nu_mincnorm_4_dxyz.mnc /tmp/bestlinreg.pl-fGFwUogf/Tnihpd_asym_00-02_t1w_4_dxyz.mnc /tmp/bestlinreg.pl-fGFwUogf/S15331_001_MNI152maskedout_RAS_nu_mincnorm_4.xfm\n",
"%(Package mni_autoreg 0.99.6, compiled by @harold (x86_64-unknown-linux-gnu) on Thu Jan 20 17:08:53 EST 2011)\n",
"\n",
"Transform_Type = Linear;\n",
"Linear_Transform =\n",
" 1.07767593860626 0.184373259544373 0.0388876646757126 -3.00531005859375\n",
" -0.168469712138176 0.921877026557922 0.297942489385605 -25.8111553192139\n",
" 0.0183407459408045 -0.314893305301666 0.984695911407471 -10.4866342544556;\n",
"" ;
float image(xspace, yspace, zspace) ;
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:valid_range = 0.f, 99.98685f ;
image:signtype = "signed__" ;
// global attributes:
:ident = "todd:neptune-ubuntu:2011.03.02.16.49.21:29928:1" ;
:history = "/usr/local/bic/bin/nu_correct 15331_001_MNI152maskedout_RAS.mnc 15331_001_MNI152maskedout_RAS_nu.mnc\n",
"Fri Feb 25 16:36:02 2011>>> minccalc -clobber -expression ((A[0] < 0.06380040559) ? 0.0 : (A[0] > 212.3628689) ? 1.0 : (A[0]-0.06380040559)/212.29906849441) * 100 + 0; 15331_001_MNI152maskedout_RAS_nu.mnc 15331_001_MNI152maskedout_RAS_nu_mincnorm.mnc\n",
"Wed Mar 2 16:49:21 2011>>> mincresample -clobber -like ../nihpd_asym_00-02_t1w.mnc -transformation 15331_001_MNI152maskedout_RAS_nu_mincnorm-reg_nihpd_bestlinreg.xfm 15331_001_MNI152maskedout_RAS_nu_mincnorm.mnc 15331_001_MNI152maskedout_RAS_nu_mincnorm-reg_nihpd_bestlinreg.mnc\n",
"" ;
data:
rootvariable = _ ;
xspace = 0 ;
yspace = 0 ;
zspace = 0 ;
image-max = 1.17549435082229e-36, 1.17549435082229e-36,
1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36,
1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36,
1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36,
1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36,
1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36,
1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36,
1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36,
1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36,
1.17549435082229e-36, 1.55469995539387, 6.33278886872083,
7.08308779408386, 8.86992227099348, 10.0161254301613, 10.1063879633967,
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