I would like to correct and restate my previous questions, hoping to be a bit more specific.


(1) This is self-response. 3dretroicor seems to do recognize slice order information in NIfTI header (I generated several patterns of 'slice_code' and 'slice_duration' in NIfTI header and checked resultant images (after converted to NIFTI_PAIR format) using 'diff' and found that those images are sometimes different. But I am not quite sure.) May I have suggestion if there are tips or pitfalls using 3dretroicor on NIfTI-format images?


(2) Below is header information for second question regarding slice order information change (?) during conversion of AFNI BRIK to NIFTI.

-- generate AFNI format

to3d -prefix ${OutPrefix}_run_013 \
-time:zt 3 1000 0.2sec alt+z \
-@ < dimon.files.run.013

-- some information from generated AFNI HEAD

type = integer-attribute
name = TAXIS_NUMS
count = 8
1000 3 77002 -999 -999
-999 -999 -999

type = float-attribute
name = TAXIS_FLOATS
count = 8
0 0.2 0 25.19741 1.6
-999999 -999999 -999999

type = float-attribute
name = TAXIS_OFFSETS
count = 3
0 0.1333333 0.06666667 // Slice order looks OK here.

type = integer-attribute
name = DATASET_RANK
count = 8
3 1000 0 0 0
0 0 0

type = integer-attribute
name = DATASET_DIMENSIONS
count = 5
64 64 3 0 0

-- Images were converted to NIfTI format using 3dAFNItoNIFTI

-- Part of output from 'nifti_tool -disp_hdr -in_files OutBrick_run_013.nii'

header file 'OutBrick_run_013.nii', num_fields = 43

name offset nvals values
------------------- ------ ----- ------
dim_info 39 1 48
dim 40 8 4 64 64 3 1000 1 1 1
slice_start 74 1 1
slice_end 120 1 2
slice_code 122 1 2 // (value 2 == sequential decreasing ??)


I found possible inconsistency in slice_code.
Since I am very new to both AFNI and NIfTI, I am not sure whether just my interpretation is wrong or there is someting wrong on header information.
Any comments will be very appreciated.

Toshi