no ap_sepscl.sag.png for fat_proc_select_vols

AFNI Message Board
1

Hi
I am trying to run

set path_P_ss = data_proc/SUBJ_001

fat_proc_select_vols
-in_dwi $path_P_ss/dwi_00/ap.nii.gz
-in_img $path_P_ss/dwi_00/ap_sepscl.sag.png
-prefix $path_P_ss/dwi_01/dwi_sel_ap

However, i only have nii for dti, not dcm files. So i did not run dcm to nii, then no png for this command. Is there any command that i can generate this png using nii file?
thanks.
rujing

2

Actually, because others have been in that same situation, fat_proc_convert_dcm_dwis will do the same conveniences of centering the volume, making it a nicer orientation (RAI), and making images, but starting from NII and bvec/bvals, as if the dcm2niix(_afni) part had already been run:


fat_proc_convert_dcm_dwis  \
        -innii    study/subj-001/acq_piece_0*.nii.gz     \
        -inbvec   study/subj-001/acq_piece_0*.bvec       \
        -inbval   study/subj-001/acq_piece_0*.bval       \
        -prefix   study/subj-001/dwi_all
        -do_movie AGIF

–pt

3

Wow, it’s working.
Thanks Paul.
rujing