AFNI version info (afni -ver
):
Hello, I am using afni_proc.py to generate script for preprocessing. I have my script written like the one below. It is a simple pipeline where I'd like to apply distortion correction (with blip) and then align functional data with (1) subject's native anatomy (2) MNI template.
However, I found that the setup below seems to concatenate the transformation from epi-->anatomy, and from anatomy-->template. At the end, I can only find the outputs in template, and there is no data saved in the native anatomy space.
For the purpose to conduct two different kinds of analysis, I want to have data both in the native anatomy space, and the template. Is there a way to do that in a single afni_proc.py script?
afni_proc.py -subj_id $RESULTSDIR \
-dsets $mydata \
-copy_anat $brainmask \
-blip_forward_dset blip_for.nii.gz \
-blip_reverse_dset blip_rev.nii.gz \
-blocks tshift align tlrc volreg \
-anat_has_skull no \
-align_opts_aea -cost lpc+ZZ -giant_move \
-tlrc_base MNI152_2009_template_SSW.nii.gz \
-tlrc_NL_warp \
-volreg_base_dset MIN_OUTLIER \
-volreg_align_e2a \
-volreg_tlrc_warp \
-blip_opts_qw -noXdis -noZdis