[MINC-users] using EMMA: possible without Mex?

[Audette, Michel]

Hi Andrew, 

thanks for your kind reply. Sorry too that mine is late. I'll look around for mincsample, if it comes with the BIC toolbox. 

Cheers, 

Michel

Michel Audette, Ph.D.   
Innovation Center Computer Assisted Surgery (ICCAS)   
Semmelweisstraße 14  
Leipzig, Germany  
Phone: ++49 (0) 341 / 97 - 1 20 13  
Fax: ++49 (0) 341 / 97 - 1 20 09 
 

 


-----Original Message-----
From: minc-users-bounces at bic.mni.mcgill.ca [mailto:minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Andrew Janke
Sent: April 8, 2008 11:54 PM
To: MINC users mailing list
Subject: Re: [MINC-users] using EMMA: possible without Mex?

On Wed, Apr 9, 2008 at 12:00 AM, Audette, Michel
<Michel.Audette at medizin.uni-leipzig.de> wrote:
>  What I want is the voxel values at specific tag points, once Matlab reads the tag files, so that I can visualize these tag points in feature space.

Hi Michel,

I once wrote a program called mincsample for doing this sort of thing.
 The only spanner in the works is that I primarily wrote it for doing
random samples from files based upon a mask.  It allows you to do
things like this:

gordon:~$ mincsample -random_samples 10 -coords ~/data/me/a.mnc
-97.553589999999999804  -10.734777364705921698  -108.63487000000000648
 1.9928282597085527073
-97.553589999999999804  107.16522058039204524   -88.947370000000006485
 1.0070954451819638109
-81.616089999999999804  117.06522040784302874   -75.822370000000006485
 7.0038910505836575737
-1.9285899999999998045  62.165221364705800511   -66.447370000000006485
 46.982528419928279106
-23.491089999999999804  131.46522015686261398   -66.447370000000006485
 2.0080872816052490748
-31.928589999999999804  67.565221270588153857   -9.2598700000000064847
 38.989852750438693363
97.446410000000000196   90.965220862744999408   4.8026299999999935153
 11.996643015182726799
-111.6160899999999998   84.665220972548922873   74.177629999999993515
 1.9958800640878919808
-115.3660899999999998   58.565221427450900649   106.99012999999999352
 1.0070954451819638109
36.508910000000000196   -28.734777050980419233  122.92762999999999352   0

Where here the output is the coordinate followed by the value.

gordon:~$ mincsample -help
Command-specific options:
General options:
 -version:        print version info and exit.
 -verbose:        print out extra information.
 -quiet:          be very quiet.
 -clobber:        clobber existing files.
 -max_buffer:     maximum size of buffers (in kbytes)
                Default value: 4096
 -mask:           select voxels within the specified mask
 -mask_val:       mask value to use
                Default value: 1

Sampling Types:
 -all:            sample all the data (Default)
 -random_seed:    Random seed to use (use to get reproducible runs)
Default: use tv_usec
                Default value: -1
 -random_samples: take # random samples from the input data
                Default value: 0

Output Options:
 -sample:         Output a <mask.mnc> file of chosen points
 -outfile:        <file> for output data (Default: stdout)
 -append:         append output data to existing file
 -ascii:          Write out data as ascii strings (default)
 -double:         Write out data as double precision floating-point values
 -coords:         Write out world co-ordinates as well as values

Generic options for all commands:
 -help:           Print summary of command-line options and abort
 -version:        Print version number of program and exit

Usage: mincsample [options] <in1.mnc> <in2.mnc> ...
       mincsample -help

The help output is above, so in essence if you can convert your tag
points to a mask then all you would need to do is this:

   mincsample -coords -ascii -mask tag_mask.mnc infile.mnc

if you wanted output like the above example. If you wanted to save a
bit of space and output in double then just swap the -ascii flag with
a -double.   You can find mincsample (in deb and source form) on
packages.bic.mni.mcgill.ca.

Let me know if you need any more help with it, the simple answer here
is that I should add tag support to mincsample (Anders Rodell is
already requesting this!) but just haven't got to it yet... :)


a
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