You can check that it added the label table to the nifti file by looking at it in a text viewer (less). I don't know much about label volumes in caret5, there appears to be some code that should try to read the label table from that extension, but I'm not sure what to do to make it happy. Workbench should display it just fine, though that might not help you.
Tim On Wed, May 29, 2013 at 8:52 PM, 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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