afni.nimh.nih.gov

Hi Ruyuan-

PTaylor and I got it working after a few tries. The major thing is to Zeropad your input. Basic flow of our test was to skullstrip your anatomical, zero pad the EPI and then align using 3dAllineate.

@SSwarper -input C1051_SurfVol.nii.gz -base MNI152_2009_template_SSW.nii.gz -subid Subj01 -skipwarp
3dZeropad -I 20 -P 20 -A 5 -prefix epi1_rs.nii.gz epi_mean_test.nii.gz 

#Align anat to EPI
 3dAllineate \
 -base  epi1_rs.nii.gz \
 -input anatSS.Subj01.nii \
 -prefix tmp.anat.aligned.nii.gz \
 -1Dmatrix_save epi1_rs_al_12.1D \
 -cost lpc \
 -final wsinc5 \
 -source_automask -autoweight \
 -twopass \
 -verb

#invert transform
cat_matvec epi1_rs_al_12.1D -I > epi2anat_12.1D

#apply inverted transform
3dAllineate -base C1051_SurfVol.nii.gz -input epi1_rs.nii.gz -1Dmatrix_apply epi2anat_12.1D -prefix epi_aligned.nii.gz

Let us know if you have other questions or troubles!

-PM



Edited 3 time(s). Last edit at 06/20/2019 11:08PM by Peter Molfese.