Dear Yunxia,

You bring up some very relevant issues. I will take a quick stab at addressing them (others please chime in/correct me as desired):

1) The images were all put into a uniform orientation to facilitate management of an otherwise unwieldy data-set (these came to us in many forms). It is important to note that reorientation did not involve any resampling or reslicing of the data that would alter the relationship between slices. If my memory serves me correct, none of the datasets were coronal or sagittal acquisitions (you can verify this by looking at each site and seeing that the x and y directions have the highest resolutions). The specific AFNI commands used for reorienting the data were "3drefit -deoblique", followed by "3dresample -orient RPI". Unfortunately, the data-preparation process knocks out the slice-timing info from the headers - as such, this info is not reliable in the headers for files on the site, though you can find the info in the release table under docs.

2) In FSL, slice order information is solely specified in the command (i.e., the NIFTI header is not used) - you can easily specify there. If AFNI, my impression is that 3dtshift does have a -tpattern option that you can use to force the order from the command line.

I hope that helps.

Best,
Mike