Hi I have tried what you say and it doesn't work, after applying @Align_centers the auto_warp.py stops in the affine registration:
@Align_Centers -overwrite -base ${TEMPLATEDIR}/${TEMPLATE} -dset ${SUBJ}_T1_ns_bc.nii.gz -prefix prueba.nii.gz -1Dmat_only
++ 3dcopy: AFNI version=AFNI_18.2.16 (Sep 12 2018) [64-bit]
++ 3drefit: AFNI version=AFNI_18.2.16 (Sep 12 2018) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset ./prueba.nii.gz
+ deoblique
+ loading and re-writing dataset ./prueba.nii.gz (./prueba.nii.gz in NIFTI storage)
++ 3drefit processed 1 datasets
auto_warp.py -overwrite -base ${TEMPLATEDIR}/${TEMPLATE}'[0]' -input prueba.nii.gz -skull_strip_input no
#++ auto_warp.py version: 0.04
# Output directory /bcbl/home/public/PARK_VFERRER/PREPROC/sub-029ParkEglPb/anat/awpy/
#Script is running:
mkdir /bcbl/home/public/PARK_VFERRER/PREPROC/sub-029ParkEglPb/anat/awpy/
cd /bcbl/home/public/PARK_VFERRER/PREPROC/sub-029ParkEglPb/anat/awpy/
#Script is running (command trimmed):
3dcopy /bcbl/home/public/PARK_VFERRER/PREPROC/sub-029ParkEglPb/anat/prueba.nii.gz ./anat.nii
++ 3dcopy: AFNI version=AFNI_18.2.16 (Sep 12 2018) [64-bit]
#Script is running (command trimmed):
3dUnifize -GM -input ./anat.nii -prefix ./anat.un.nii
++ 3dUnifize: AFNI version=AFNI_18.2.16 (Sep 12 2018) [64-bit]
+ Pre-processing: ADV......UWGm
++ Output dataset ./anat.un.nii
++ ===== Elapsed = 35.7 sec
#Script is running (command trimmed):
3dcopy /export/home/vferrer/public/PARK_VFERRER/TEMPLATES_ATLAS/MNI152_2009_template_flip.nii.gz ./base.nii
++ 3dcopy: AFNI version=AFNI_18.2.16 (Sep 12 2018) [64-bit]
#++ Aligning /bcbl/home/public/PARK_VFERRER/PREPROC/sub-029ParkEglPb/anat/awpy/base.nii data to /bcbl/home/public/PARK_VFERRER/PREPROC/sub-029ParkEglPb/anat/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_XYZ_OYmeqfZ3JqF7n9LNC7gDAA
++ 3dcopy: AFNI version=AFNI_18.2.16 (Sep 12 2018) [64-bit]
Performing center alignment with @Align_Centers
++ 3dcopy: AFNI version=AFNI_18.2.16 (Sep 12 2018) [64-bit]
++ 3drefit: AFNI version=AFNI_18.2.16 (Sep 12 2018) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset ./anat.un_XYZ_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig
+ deoblique
++ 3drefit processed 1 datasets
++ 3drename: AFNI version=AFNI_18.2.16 (Sep 12 2018) [64-bit]
++ THD_rename_dataset_files: rename anat.un_XYZ_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig.HEAD -> __ats_tmp__anat.un_XYZ_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig.HEAD
++ THD_rename_dataset_files: rename anat.un_XYZ_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig.BRIK -> __ats_tmp__anat.un_XYZ_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig.BRIK
** THD_rename_dataset_files: old header anat.un_XYZ_OYmeqfZ3JqF7n9LNC7gDAA_shft+acpc.HEAD doesn't exist!
** THD_rename_dataset_files: old header anat.un_XYZ_OYmeqfZ3JqF7n9LNC7gDAA_shft+tlrc.HEAD doesn't exist!
++ 3dWarp: AFNI version=AFNI_18.2.16 (Sep 12 2018) [64-bit]
++ Authored by: RW Cox
Center distance of 0.000000 mm
Padding ...
++ 3dZeropad: AFNI version=AFNI_18.2.16 (Sep 12 2018) [64-bit]
++ output dataset: ./__ats_tmp__ref_base.nii_40pad+orig.BRIK
Resampling ...
++ 3dcalc: AFNI version=AFNI_18.2.16 (Sep 12 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__ats_tmp__resamp_step+orig.BRIK
++ 3dcalc: AFNI version=AFNI_18.2.16 (Sep 12 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__ats_tmp__resamp+orig.BRIK
Clipping -0.000100 3185.330100 ...
++ 3dcalc: AFNI version=AFNI_18.2.16 (Sep 12 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./__ats_tmp___rs_pre.anat.un_XYZ_OYmeqfZ3JqF7n9LNC7gDAA+orig.BRIK
++ 3drefit: AFNI version=AFNI_18.2.16 (Sep 12 2018) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp___rs_pre.anat.un_XYZ_OYmeqfZ3JqF7n9LNC7gDAA+orig.HEAD
+ Didn't make any changes for dataset __ats_tmp___rs_pre.anat.un_XYZ_OYmeqfZ3JqF7n9LNC7gDAA+orig.HEAD !
++ 3drefit processed 1 datasets
++ 3drefit: AFNI version=AFNI_18.2.16 (Sep 12 2018) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp__resamp_NN+orig.HEAD
+ Didn't make any changes for dataset __ats_tmp__resamp_NN+orig.HEAD !
++ 3drefit processed 1 datasets
++ 3drefit: AFNI version=AFNI_18.2.16 (Sep 12 2018) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp__resamp_edge_art+orig.HEAD
+ Didn't make any changes for dataset __ats_tmp__resamp_edge_art+orig.HEAD !
++ 3drefit processed 1 datasets
Registration (linear final interpolation) ...
++ 3dWarpDrive: AFNI version=AFNI_18.2.16 (Sep 12 2018) [64-bit]
++ Authored by: RW Cox
RMS[0] = 501.667 415.306 ITER = 137/137
501.667
Warping used up maximum iterations of 137
Convergence might not have
been reached.
Doubling number of iterations
++ 3drename: AFNI version=AFNI_18.2.16 (Sep 12 2018) [64-bit]
++ THD_rename_dataset_files: rename __ats_tmp__reg_warpdriveout+orig.HEAD -> __ats_tmp__reg_warpdriveout_maxed_iters+orig.HEAD
++ THD_rename_dataset_files: rename __ats_tmp__reg_warpdriveout+orig.BRIK -> __ats_tmp__reg_warpdriveout_maxed_iters+orig.BRIK
++ 3dWarpDrive: AFNI version=AFNI_18.2.16 (Sep 12 2018) [64-bit]
++ Authored by: RW Cox
RMS[0] = 501.667 415.306 ITER = 274/274
501.667
Warping used up maximum iterations
even after doubling number of iterations to 274.
Convergence might not have been reached.
If you find the alignment poor, try
rerunning the script with a transform
type of fewer parameters (-xform) or by using
an even higher number of iterations (-maxite).
You can also choose to continue with the
current result (dset: __ats_tmp__reg_warpdriveout+orig
by using the option: -OK_maxite
Script will stop ...
#**ERROR Failed in affine step
** ERROR - script failed
I have checked and the images are touching each other after the Align_centers (obviusly) and if you notice, this was already incorporated in the auto_warp.py pipeline. Is there any alternative i can use in this subject for the wrapping?. Thanks in adavance,
Vicente
