Thanks! This did not get the error out.
Anyway, but I was also trying to register the anatomic with the functional using the following
align_epi_anat.py -anat ../MPRAGEco.nii.gz -epi_base 0 -epi ../Imagination.nii.gz -master_anat ../Imagination.nii.gz -ginormous_move -align_centers yes -save_vr
but I get an error in 3dAllineate. Is it because the functional dataset is a 4-volume dataset when passed in as an argument to -master_anat?
.............
#Script is running (command trimmed):
cat_matvec -ONELINE ./MPRAGEco_al_e2a_only_mat.aff12.1D ./__tt_MPRAGEco_ns_shft_I.1D -I > ./MPRAGEco_al_mat.aff12.1D
#++ Combining anat to epi and oblique transformations
#Script is running (command trimmed):
3dAllineate -base ./__tt_Imagination_vr_ts_ns+orig -1Dmatrix_apply ./MPRAGEco_al_mat.aff12.1D -prefix ./MPRAGEco_al -input ./__tt_MPRAGEco_ns+orig -master ../Imagination.nii.gz -twobest 11 -twopass -VERB -maxrot 45 -maxshf 40 -fineblur 1 -source_automask+2
++ 3dAllineate: AFNI version=AFNI_2011_12_21_1014 (Mar 23 2015) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./__tt_MPRAGEco_ns+orig.HEAD
++ Base dataset: ./__tt_Imagination_vr_ts_ns+orig.HEAD
++ Loading datasets
++ NOTE: base and source coordinate systems have different handedness
+ Orientations: base=Left handed (RPI); source=Right handed (LPI)
+ Range param#4 [z-angle] = -45.000000 .. 45.000000
+ Range param#5 [x-angle] = -45.000000 .. 45.000000
+ Range param#6 [y-angle] = -45.000000 .. 45.000000
+ Range param#1 [x-shift] = -40.000000 .. 40.000000
+ Range param#2 [y-shift] = -40.000000 .. 40.000000
+ Range param#3 [z-shift] = -40.000000 .. 40.000000
++ ========== Applying transformation to 1 sub-bricks ==========
++ Memory usage now = 826,000 (826 thousand [kilo]): about to start alignment loop
++ ========== sub-brick #0 ========== [total CPU to here=0.0 s]
+ * Enter alignment setup routine
+ - copying base image
+ - copying source image
+ - no weight image
+ - using 11 points from base image [use_all=0]
+ * Exit alignment setup routine
++ using -1Dmatrix_apply
++ Computing output image
++ image warp: parameters = -2.2243 0.2937 -1.1725 111.6654 0.9821 3.7125 -1.1005 -68.1735 -1.4778 1.3757 3.7100 67.7136
++ Memory usage now = 20,051,187 (20 million [mega]): end of sub-brick alignment
++ Memory usage now = 580,603 (581 thousand [kilo]): end of sub-brick loop (after cleanup)
++ Output dataset ./MPRAGEco_al+orig.BRIK
++ Memory usage now = 336,513 (337 thousand [kilo]): after writing output dataset
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 0.3
++ Memory usage now = 211,753 (212 thousand [kilo]): end of program (after final cleanup)
++ ###########################################################
#**ERROR Could not square a circle (3dAllineate could not align anat to epi)
Traceback (most recent call last):
File "/home/maitra/abin/align_epi_anat.py", line 3245, in <module>
ps.align_anat2epi(e, a, ps.epi_wt, ps.AlOpt, suff, mcost)
TypeError: 'NoneType' object is not iterable
