hello
I am attempting to run auto_warp.py to correct for alignment problems and I keep getting the following error.
can anyone tell me what I am doing wrong or is there a way to fix this problem?
Warning:***************************
Registration did not converge, even
without shear operation.
Check your results, the -help tips
and report persisting problems to
progam authors.
Script will stop ...
#**ERROR Failed in affine step
** ERROR - script failed
thank you for any help with this matter.
here is the output up to that point:
#++ auto_warp.py version: 0.06
# Output directory /data/mprc_data1/home/jwest/IRT_Mark_Data/fMRI_data/S0296_reload/anat/awpy/
#Script is running (command trimmed):
mkdir ./awpy/
cd /data/mprc_data1/home/jwest/IRT_Mark_Data/fMRI_data/S0296_reload/anat/awpy/
#Script is running (command trimmed):
3dcopy /data/mprc_data1/home/jwest/IRT_Mark_Data/fMRI_data/S0296_reload/anat/warped+orig ./anat.nii
++ 3dcopy: AFNI version=AFNI_22.3.07 (Dec 2 2022) [64-bit]
#Script is running (command trimmed):
3dUnifize -GM -input ./anat.nii -prefix ./anat.un.nii
++ 3dUnifize: AFNI version=AFNI_22.3.07 (Dec 2 2022) [64-bit]
+ Pre-processing: ADV.......................UW[s546381]Gm
++ Output dataset ./anat.un.nii
++ ===== Elapsed = 53.2 sec
#Script is running (command trimmed):
3dcopy /data/mprc_data1/home/jwest/afni/MNI_avg152T1+tlrc ./base.nii
++ 3dcopy: AFNI version=AFNI_22.3.07 (Dec 2 2022) [64-bit]
#++ Aligning /data/mprc_data1/home/jwest/IRT_Mark_Data/fMRI_data/S0296_reload/anat/awpy/base.nii data to /data/mprc_data1/home/jwest/IRT_Mark_Data/fMRI_data/S0296_reload/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_AFN_OYmeqfZ3JqF7n9LNC7gDAA
++ 3dcopy: AFNI version=AFNI_22.3.07 (Dec 2 2022) [64-bit]
Performing center alignment with @Align_Centers
++ 3dcopy: AFNI version=AFNI_22.3.07 (Dec 2 2022) [64-bit]
++ 3drefit: AFNI version=AFNI_22.3.07 (Dec 2 2022) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset ./anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig
+ deoblique
++ 3drefit processed 1 datasets
++ 3drename: AFNI version=AFNI_22.3.07 (Dec 2 2022) [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 -> __ats_tmp__anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig.BRIK
** 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_22.3.07 (Dec 2 2022) [64-bit]
++ Authored by: RW Cox
++ anat already stripped, re-using
Center distance of 0.000046 mm
Padding ...
++ 3dZeropad: AFNI version=AFNI_22.3.07 (Dec 2 2022) [64-bit]
++ output dataset: ./__ats_tmp__ref_base.nii_15pad+tlrc.BRIK
Resampling ...
++ 3dcalc: AFNI version=AFNI_22.3.07 (Dec 2 2022) [64-bit]
++ Authored by: A cast of thousands
++ 3dcalc: AFNI version=AFNI_22.3.07 (Dec 2 2022) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__ats_tmp__resamp+tlrc.BRIK
Clipping -0.000100 1538.960100 ...
++ 3dcalc: AFNI version=AFNI_22.3.07 (Dec 2 2022) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./__ats_tmp___rs_pre.anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA+tlrc.BRIK
++ 3drefit: AFNI version=AFNI_22.3.07 (Dec 2 2022) [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_22.3.07 (Dec 2 2022) [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_22.3.07 (Dec 2 2022) [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 (cubic final interpolation) ...
++ 3dWarpDrive: AFNI version=AFNI_22.3.07 (Dec 2 2022) [64-bit]
++ Authored by: RW Cox
++ Initial scale factor set to 0.30/462.30=1.6e+03
RMS[0] = 0.28487 0.295696 ITER = 8/50
0.28487
Warning:*****************************
Registration did not converge, trying
registration without shearing.
++ 3drename: AFNI version=AFNI_22.3.07 (Dec 2 2022) [64-bit]
++ THD_rename_dataset_files: rename __ats_tmp__reg_warpdriveout+orig.HEAD -> __ats_tmp__reg_warpdriveout_NoConvergence+orig.HEAD
++ THD_rename_dataset_files: rename __ats_tmp__reg_warpdriveout+orig.BRIK -> __ats_tmp__reg_warpdriveout_NoConvergence+orig.BRIK
++ 3dWarpDrive: AFNI version=AFNI_22.3.07 (Dec 2 2022) [64-bit]
++ Authored by: RW Cox
++ Initial scale factor set to 0.30/462.30=1.6e+03
RMS[0] = 0.28487 0.299927 ITER = 12/50
0.28487
Warning:***************************
Registration did not converge, even
without shear operation.
Check your results, the -help tips
and report persisting problems to
progam authors.
Script will stop ..
