/etc/voxbo/jobtypes/spm2_norm_calc.vjt is in voxbo 1.8.5~svn1246-1ubuntu1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 | shortname spm2_norm_calc
description SPM2 Normalization -- calculate parameters
invocation script
requires cpu
requires matlab
retry_tag Try again later
setenv MATLABPATH=$(SPM2_PATH)
setenv HOME=/tmp
argument
name=dir
argdesc=directory
type=string
default=none
low=none
high=none
end
argument
name=paramfile
argdesc=file containing params
type=string
default=none
low=none
high=none
end
argument
name=infile
argdesc=your volume
type=string
default=none
low=none
high=none
end
argument
name=refvolume
argdesc=reference volume
type=string
default=none
low=none
high=none
end
argument
name=vox_x
argdesc=vox_x size
type=long
default=none
low=none
high=none
end
argument
name=vox_y
argdesc=vox_y size
type=long
default=none
low=none
high=none
end
argument
name=vox_z
argdesc=vox_z size
type=long
default=none
low=none
high=none
end
argument
name=bb
argdesc=bounding box
type=string
default=none
low=none
high=none
end
command vb2img $(dir)/$(infile) $(dir)/tmp_spm2norm.img
# for fun, add -logfile /jet/kimberg/test/spmnorm/matlab.log
command $(SPM2_MATLAB_CMD)
| spm_defaults;
| global defaults;
| cd $(dir);
| defaults.normalise.write.vox=[$(vox_x) $(vox_y) $(vox_z)];
| defaults.normalise.write.interp=7;
| defaults.normalise.write.wrap=[0 0 0];
| defaults.normalise.write.bb=$(bb);
| VG=spm_vol('$(refvolume)')
| V=spm_vol('$(dir)/tmp_spm2norm.img')
| params=spm_normalise(VG,V,'$(dir)/$(paramfile)','','',defaults.normalise.estimate);
| msk=spm_write_sn(V,params,defaults.normalise.write,'mask');
| spm_write_sn(V,params,defaults.normalise.write,msk);
| exit
command vb2cub $(dir)/wtmp_spm2norm.img $(dir)/n$(infile)
command /bin/rm $(dir)/tmp_spm2norm.img $(dir)/tmp_spm2norm.hdr
command /bin/rm $(dir)/wtmp_spm2norm.img $(dir)/wtmp_spm2norm.hdr
command test -e $(dir)/$(paramfile)
|