to3d hdr/img

AFNI Message Board
1

Hi AFNI experts,
I was given some ANALYZE data (hdr/img files) and need to convert them into AFNI format for further analysis.
Howver, even when trying to convert only 2 volumes, “to3d” complains about the slice number which I don’t understand. Please see the following details:

3dinfo file1.hdr
R-to-L extent: -83.772 [R] -to- 105.228 [L] -step- 3.000 mm [ 64 voxels]
A-to-P extent: -93.242 [A] -to- 95.758 [P] -step- 3.000 mm [ 64 voxels]
I-to-S extent: -85.910 [I] -to- 50.090 [S] -step- 4.000 mm [ 35 voxels]

3dinfo file2.hdr
R-to-L extent: -83.754 [R] -to- 105.246 [L] -step- 3.000 mm [ 64 voxels]
A-to-P extent: -93.199 [A] -to- 95.801 [P] -step- 3.000 mm [ 64 voxels]
I-to-S extent: -85.987 [I] -to- 50.013 [S] -step- 4.000 mm [ 35 voxels]

to3d -prefix ttt -orient RPI -time:zt 35 2 2000 file1.hdr file2.hdr
++ to3d: AFNI version=AFNI_16.2.07 (Aug 2 2016) [64-bit]
++ Authored by: RW Cox
++ It is best to use to3d via the Dimon program.
*+ WARNING: TR expressed in milliseconds will be converted to TR=2.000000s
** Unknown tpattern = file1.hdr
++ Counting images: total=35 2D slices
** Number of slices on command line = 35
** Number of slices needed for -time: = 70
** Something is wrong with your command line!

So, while my inputs are 2 volumes with each having 35 slices, how come AFNI only find 35 slices in total? I also noticed that the values of “R-to-L”, “A-to-P”, and “I-to-S” are slightly different between volumes. Could this be the problem? My understanding is that AFNI will take these “extent” values from the 1st volume in the input list and ignore the rest, am I correct?

Thank you very much for your help!

2

It may be confusing to give to3d hdr files instead of
img files. But in any case, try 3dTcat directly, then
see what 3dinfo says about the result.

3dTcat -DAFNI_ANALYZE_ORIENT=RPI -tr 2 -tpattern alt+z \
       -prefix NEW file1.hdr file2.hdr
3dinfo NEW+orig
  • rick