There is the nifti c library: http://niftilib.sourceforge.net/
I haven't really looked at it, so I don't know how easy it makes it, but even just the nifti1 header has enough documentation (and the format is simple enough) that you could write your own, if you are so inclined. Tim On Wed, May 29, 2013 at 9:50 PM, Colin Reveley <[email protected]> wrote: > Is there any code anywhere to just open a nifti header with caret > extensions and just mess with those extensions in a programming language? > (C is a programming language. C would be fine. Optimal possibly) > > since when one loads a paint volume you can generate a header with names > "region_1 region_2 etc" and those integers correspond to the voxel values > caret has read then: then one could just substitute those names for the > names that are actually required. > > I just don't know how to access the header (the caret label volume > specific bit). > > Come what may, it might behove us to have a robust, controlled (by us) > distributable method of doing this in software that we can be confident > of distributing to users in a way that is automated. > > Good Software Engineering Practice. Or something. > > best, > > Colin > > > > > > On 30 May 2013 02:52, Colin Reveley <[email protected]> wrote: > >> Hi - >> >> re: wb_command -volume-label-import >> >> what it appears to do is just vaporize the header. >> >> However, much could have gone wrong. The input volume is wholly >> constructed in software (mainly imageJ and inhouse C) and is probably weird >> (although it's been saved in CARET before trying to run this. I tried both >> ways. header below has been through caret). and maybe I've got the format >> of the label list wrong. >> >> I note that the output of the command is a float volume. I was pretty >> sure paint volumes had to be unsigned char. I tried both float and uchar as >> inputs anyway. >> >> my input header looks something like this. and my label file looks like >> what follows under the header >> >> thanks for advice >> >> I appreciate it may not work. That is ok. It was a bit too good to be >> true anyway. it doesn't dump core, or give an error (or any info at all). >> it just thinks for a bit, removes most info from the header and outputs a >> float volume >> >> actually there's probably a debug swtich. I'll look at that now. >> >> thanks, >> >> Colin >> >> sizeof_hdr: 348 >> data_type: >> db_name: >> extents: 0 >> session_error: 0 >> regular: r >> dim_info: 0 >> dim: 3 137 347 245 1 1 0 0 >> intent_p1: 0.000 >> intent_p2: 0.000 >> intent_p3: 0.000 >> intent_code: 1002 >> datatype: 2 >> bitpix: 0 >> slice_start: 0 >> pixdim: 1.000 0.250 0.250 0.250 0.000 0.000 0.000 0.000 >> vox_offset: 41760.000 >> scl_slope: 1.000 >> scl_inter: 0.000 >> slice_end: 0 >> slice_code: 0 >> xyzt_units: 0 >> cal_max: 0.000 >> cal_min: 0.000 >> slice_duration: 0.000 >> toffset: 0.000 >> glmax: 0 >> glmin: 0 >> description: >> >> aux_file: >> qform_code: 3 >> sform_code: 3 >> quatern_b: 0.000 >> quatern_c: 0.000 >> quatern_d: 0.000 >> qoffset_x: -2.750 >> qoffset_y: -48.750 >> qoffset_z: -26.500 >> srow_x: 0.250 0.000 0.000 -2.750 >> srow_y: 0.000 0.250 0.000 -48.750 >> srow_z: 0.000 0.000 0.250 -26.500 >> intent_name: >> magic: n+1 >> >> Intent Name: NIFTI_INTENT_LABEL >> Intent Parameters:Label index >> >> First Voxel XYZ (method 1): 0.000, 0.000, 0.000 >> Spacing: 0.250, 0.250, 0.250 >> >> QFORM: NIFTI_XFORM_TALAIRACH >> 1.000 0.000 0.000 0.000 >> 0.000 1.000 0.000 0.000 >> 0.000 0.000 1.000 0.000 >> 0.000 0.000 0.000 1.000 >> Orientation: Left to Right, Posterior to Anterior, Inferior to Superior >> First Voxel XYZ (Method 2): -2.750, -48.750, -26.500 >> Spacing: 0.250, 0.250, 0.250 >> >> SFORM: NIFTI_XFORM_TALAIRACH >> 0.250 0.000 0.000 -2.750 >> 0.000 0.250 0.000 -48.750 >> 0.000 0.000 0.250 -26.500 >> 0.000 0.000 0.000 1.000 >> Orientation: Left to Right, Posterior to Anterior, Inferior to Superior >> First Voxel XYZ (Method 3): -2.750, -48.750, -26.500 >> Spacing: 0.250, 0.250, 0.250 >> >> Data Type: NIFTI_TYPE_UINT8 >> >> Space Units: NIFTI_UNITS_UNKNOWN >> Time Units: NIFTI_UNITS_UNKNOWN >> >> Extension 1 before byte swap >> Size: 22816 >> Code: 4 >> Extension 1 after byte swap >> Size: 22816 >> Code: 4 >> AFNI extension: >> Extension 2 before byte swap >> Size: 18592 >> Code: 30 >> Extension 2 after byte swap >> Size: 18592 >> Code: 30 >> >> >> --- >> >> F3 >> 107 50 5 240 255 >> 8Bm >> 77 50 10 5 255 >> ABmc >> 31 50 10 155 255 >> Ig >> 51 50 30 115 255 >> G >> 161 50 30 140 255 >> Ld >> 119 50 40 45 255 >> LIPv >> 20 50 40 120 255 >> Ia >> 87 50 55 15 255 >> >> >> > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > >
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