Dear Afni,

I am encountering some problems of importing the functionals from FSL into afni/suma. Everytime I tried to convert or tranform the functionals I got from FSL (eg. example_func.nii, zstat.nii, etc), I got the error message almost everytime.

sform was not exact, and the worst axis is
5.100004 degrees from plumb.
qform not present, sform used.
sform was not exact, and the worst axis is
5.100004 degrees from plumb.
...

All the EPI were acquired in axial slicese, so I didnt intend to deoblique them.

And I am wondering if the imcomplete info of sform and qform will affect the analysis to some degree.

My intention is to register the zstat from FSL onto the skullstriped T1 for each person, and produce the average of the functinoals and anatomicals. But somehow the alignment seems not quite good.

here are the steps I used

3dSkullStrip -input na1.nii -orig_vol -prefix s_ana1
3dresample -prefix zstat_to_ASR -orient ASR -inset zstat.nii
3dresample -prefix example_func_to_ASR -orient ASR -inset example_func
3dAllineate -base ss_ana1 -1Dmatrix_save MMM.1D -input example_func_to_ASR
3dAllineate -master ss_ana1 -1Dmatrix_apply MMM.1D -input zstat_to_ASR -cost mi -prefix zstat_reg_to_ssana

Are they looking correct?
I reoriented the example_fun and zstat (coz they were all in LPI).

Thank you for any suggestions

cheers,
Jackie