Hi Peter,
Thank you for your response. Actually, your answer reminded me a warning information about deoblique at the beginning when I ran auto_warp.py. Then I took anther version of T1 image (skull stripped) from Freesurfer and the result of inverse warping looks reasonable now, although it is still a little off, but I think that might be due to the alignment between T1 and template.
I would still like to post the terminal output here, to see if you could help to check everything looks normal. Thanks! The AFNI version I used is AFNI_19.0.24 (Mar 8 2019)
Below are the terminal output for auto_warp.py
[Qiuhais-MacBook-Pro-2:~/jin/5006] qiuhai% auto_warp.py -base MNI_T1_ns.nii -input brain.nii -skull_strip_input no
#++ auto_warp.py version: 0.04
# Output directory /Users/qiuhai/jin/5006/awpy/
#Script is running:
mkdir /Users/qiuhai/jin/5006/awpy/
cd /Users/qiuhai/jin/5006/awpy/
#Script is running:
3dcopy /Users/qiuhai/jin/5006/brain.nii /Users/qiuhai/jin/5006/awpy/anat.nii
++ 3dcopy: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
#Script is running (command trimmed):
3dUnifize -GM -input ./anat.nii -prefix ./anat.un.nii
++ 3dUnifize: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
+ Pre-processing: ADV.....UWGm
++ Output dataset ./anat.un.nii
++ ===== CPU time = 51.8 sec Elapsed = 12.1
#Script is running:
3dcopy /Users/qiuhai/jin/5006/MNI_T1_ns.nii /Users/qiuhai/jin/5006/awpy/base.nii
++ 3dcopy: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
#++ Aligning /Users/qiuhai/jin/5006/awpy/base.nii data to /Users/qiuhai/jin/5006/awpy/anat.un.nii data
#Script is running (command trimmed):
@auto_tlrc -base ./base.nii -input ./anat.un.nii -suffix .aff -no_ss -no_pre -init_xform CENTER
Copying NIFTI volume to ./anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA
++ 3dcopy: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
Performing center alignment with @Align_Centers
++ 3dcopy: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ 3drefit: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset ./anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig
+ deoblique
++ 3drefit processed 1 datasets
++ 3drename: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ THD_rename_dataset_files: rename anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig.HEAD -> __ats_tmp__anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig.HEAD
++ THD_rename_dataset_files: rename anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig.BRIK.gz -> __ats_tmp__anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig.BRIK.gz
** THD_rename_dataset_files: old header anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA_shft+acpc.HEAD doesn't exist!
** THD_rename_dataset_files: old header anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA_shft+tlrc.HEAD doesn't exist!
++ 3dWarp: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: RW Cox
Center distance of 0.000015 mm
Padding ...
++ 3dZeropad: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ output dataset: ./__ats_tmp__ref_base.nii_40pad+tlrc.BRIK
Resampling ...
++ 3dcalc: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: A cast of thousands
++ 3dcalc: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: A cast of thousands
Clipping -0.000100 1566.890100 ...
++ 3dcalc: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: A cast of thousands
++ 3drefit: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp___rs_pre.anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA+tlrc.HEAD
+ changing dataset view code
+ Changed dataset view type and filenames.
++ 3drefit processed 1 datasets
++ 3drefit: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp__resamp_NN+tlrc.HEAD
+ changing dataset view code
+ Changed dataset view type and filenames.
++ 3drefit processed 1 datasets
++ 3drefit: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp__resamp_edge_art+tlrc.HEAD
+ changing dataset view code
+ Changed dataset view type and filenames.
++ 3drefit processed 1 datasets
Registration (linear final interpolation) ...
++ 3dWarpDrive: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: RW Cox
RMS[0] = 1884.17 851.388 ITER = 14/137
1884.17
Warping has converged.
++ 3dcopy: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ 3dWarp: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: RW Cox
Applying brain mask
++ 3dcalc: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: A cast of thousands
++ 3dWarp: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: RW Cox
++ 3drename: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ THD_rename_dataset_files: rename __ats_tmp___pad40_pre.anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA.aff+orig.HEAD -> __ats_tmp___pad40_pre.anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA.aff.skl+orig.HEAD
++ THD_rename_dataset_files: rename __ats_tmp___pad40_pre.anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA.aff+orig.BRIK.gz -> __ats_tmp___pad40_pre.anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA.aff.skl+orig.BRIK.gz
++ 3dcalc: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: A cast of thousands
Unpadding ...
++ 3dZeropad: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ output dataset: ./__ats_tmp___upad40_pre.anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA.aff+orig.BRIK
++ 3drefit: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp___upad40_pre.anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA.aff+orig
*+ WARNING: Changing the space of an ORIG view dataset may cause confusion!
*+ WARNING: NIFTI copies will be interpreted as TLRC view (not TLRC space).
*+ WARNING: Consider changing the view of the dataset to TLRC view also
++ 3drefit processed 1 datasets
Changing view of transformed anatomy
++ 3drefit: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp___upad40_pre.anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA.aff+orig.HEAD
+ changing dataset view code
+ Changed dataset view type and filenames.
++ 3drefit processed 1 datasets
Setting parent with 3drefit -wset ./anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA+orig.HEAD __ats_tmp___upad40_pre.anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA.aff+tlrc
++ 3drefit: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp___upad40_pre.anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA.aff+tlrc
+ setting Warp parent
++ 3drefit processed 1 datasets
++ 3dAFNItoNIFTI: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
Cleanup ...
++ 3drename: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Warning: ignoring +orig on new_prefix.
++ THD_rename_dataset_files: rename __ats_tmp___rs_pre.anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA+orig.HEAD -> __ats_tmp___rs_pre.anat.un+orig.HEAD
++ THD_rename_dataset_files: rename __ats_tmp___rs_pre.anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA+orig.BRIK.gz -> __ats_tmp___rs_pre.anat.un+orig.BRIK.gz
++ 3drename: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Warning: ignoring +orig on new_prefix.
++ THD_rename_dataset_files: rename pre.anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA+orig.HEAD -> pre.anat.un+orig.HEAD
++ THD_rename_dataset_files: rename pre.anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA+orig.BRIK.gz -> pre.anat.un+orig.BRIK.gz
#Script is running:
3dAttribute DELTA /Users/qiuhai/jin/5006/awpy/anat.un.aff.nii
#Script is running:
3dAttribute DELTA /Users/qiuhai/jin/5006/awpy/base.nii
2.000000 2.000000
#Script is running (command trimmed):
3dinfo -same_grid ./anat.un.aff.nii ./base.nii
#++ Aligning /Users/qiuhai/jin/5006/awpy/base.nii data to /Users/qiuhai/jin/5006/awpy/anat.un.aff.nii data
#Script is running (command trimmed):
3dQwarp -prefix ./anat.un.aff.qw.nii -blur -3 -3 -workhard:0:1 -base ./base.nii -source ./anat.un.aff.nii
++ OpenMP thread count = 12
++ 3dQwarp: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
++ Dataset zero-pad: xbot=1 xtop=2 ybot=2 ytop=5 zbot=5 ztop=0 voxels
++ Weightizing the base image
++ +++++++++++ Begin warp optimization: base=./base.nii source=./anat.un.aff.nii
++ AFNI warpomatic: 94 x 116 x 96 volume ; autobbox = 5..87 7..107 5..89 [clock= 502ms]
lev=0 0..93 0..115 0..95: [first cost=-0.81092] ..... done [cost:-0.81092==>-0.89414]
lev=1 patch=71x87x71 [clock= 11s 133ms]........:[cost=-0.94629]:........ done [cost:-0.89414==>-0.95986 ; 16 patches optimized, 0 skipped]
lev=2 patch=53x65x53 [clock= 16s 830ms]........................... done [cost:-0.95986==>-1.04325 ; 27 patches optimized, 0 skipped]
lev=3 patch=39x49x41 [clock= 22s 45ms]............... done [cost:-1.04325==>-1.11984 ; 50 patches optimized, 14 skipped]
lev=4 patch=29x37x31 [clock= 31s 648ms]................. done [cost:-1.11984==>-1.17822 ; 105 patches optimized, 45 skipped]
lev=5 patch=25x25x25 [clock= 40s 856ms]..................... done [cost:-1.17822==>-1.24541 ; 241 patches optimized, 151 skipped]
++ ========== total number of parameters 'optimized' = 5427
++ Output dataset ./anat.un.aff.qw.nii
++ Output dataset ./anat.un.aff.qw_WARP.nii
++ ===== CPU time = 333.8 sec clock time = 53s 854ms
#++ Applying warps to /Users/qiuhai/jin/5006/brain.nii
#Script is running (command trimmed):
3dNwarpApply -nwarp "./anat.un.aff.qw_WARP.nii anat.un.aff.Xat.1D" -master ./base.nii -source /Users/qiuhai/jin/5006/brain.nii -prefix ./brain.aw.nii
++ 3dNwarpApply: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: Zhark the Warped
++ -master dataset is './base.nii'
++ opened source dataset '/Users/qiuhai/jin/5006/brain.nii'
++ Processing -nwarp
++ Warping:.Z
++ Output dataset ./brain.aw.nii
++ total CPU time = 3.3 sec Elapsed = 0.5
#++ Saving history
#Script is running (command trimmed):
3dNotes -h "auto_warp.py -base MNI_T1_ns.nii -input brain.nii \
-skull_strip_input no" ./brain.aw.nii
And below is the terminal output for 3dNwarpApply that I re-ran with -iwarp option:
[Qiuhais-MacBook-Pro-2:~/jin/5006] qiuhai% 3dNwarpApply -master brain.nii -dxyz 2 -source aal_MNI_V4.nii -iwarp -nwarp "awpy/anat.un.aff.qw_WARP.nii awpy/anat.un.aff.nii.Xaff12.1D" -ainterp NN -prefix aal_MNI_V4_NL_native.nii
++ 3dNwarpApply: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: Zhark the Warped
++ -master dataset is 'brain.nii'
++ output grid size = 2 mm
++ opened source dataset 'aal_MNI_V4.nii'
++ Processing -nwarp
+ -- invert max|AA|=40.394058
+ - init nstep=7 qq=1/2^7=0.007812
+ - start iterations: normAA=28.084309 inewtfac=0.273993
+ - iterate 1 nrat=0.029783
+ - iterate 2 nrat=0.021639
+ - iterate 3 nrat=0.019353
+ - iterate 4 nrat=0.012896
+ - iterate 5 nrat=0.010630
+ - iterate 6 nrat=0.006168
+ - iterate 7 nrat=0.004342
+ - iterate 8 nrat=0.002062
+ - iterate 9 nrat=0.001304
+ - iterate 10 nrat=0.000478
+ - switching from linear interp
+ - iterate 11 nrat=0.000187
+ - iterate 12 nrat=0.000063
+ -- iteration converged
++ Warping:.Z
++ Output dataset ./aal_MNI_V4_NL_native.nii
++ total CPU time = 61.4 sec Elapsed = 7.0
