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Dear Jie, The filtered_func_data in the first level analysis should not be in standard space, as we do all of the first level analysis in the native functional space. If your registration looks good, as it does to me, and the cope images in the higher level analysis directories are correctly in standard space then it looks like everything is working fine. All the best, Mark On 31 Mar 2014, at 16:16, Jie Yu <[log in to unmask]> wrote: > Dear expert > > Sorry for the bothering again. > > But I just checked the report_reg html file of the 1st level FEAT directory. > > Although the filtered_func_data file has wrong orientation and is not in standard space, the report_reg html file seems ok??? > (please check the attached image) > > Could it be that fsl feat program automatically adjust the orientation for me so that reorientation is not necessary??? > > > > > <Screen Shot 2014-03-31 at 16.12.52.png>