Hey guys,

You are correct that the anat is a T2, it is being used since the slicing matches that of the epi. I used the TT_N27+tlrc template since it is our lab standard and I am not aware of any T2 weighted standard brain templates.

I was curious about using align_epi_anat.py and seeing whether it would put the image into full tlrc space and label the output as such. I gave it a few tries but it seems to have problems with one of the resampling steps even when -resample off option is utilized.

Script + Error message are below. Any ideas?

-Chris

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foreach subj ( 2H_test_Jeff )# 17M 18O )# 5U 6T 7U 8K 9S 10H 12N 13B 14K 15U 16Y
align_epi_anat.py -dset1to2 \
-dset2 TT_N27+tlrc \
-dset1 ${subj}_T2_CardANATrai_SS+orig \
-epi_base 0 \
-suffix _e2a \
-anat_has_skull no \
-epi_strip None \
-tshift off \
-volreg off \
-resample off \
-AddEdge | & tee ${subj}_align-py_stdout.txt

mv ${subj}_align-py_stdout.txt AddEdge
mv ${subj}_anat_brain_e2a_mat.aff12.1D AddEdge
mv ${subj}_vr_z4_e2a_mat.aff12.1D AddEdge


end

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#++ align_epi_anat version: 1.33
#++ turning off volume registration
#++ turning off resampling
#++ turning off deobliquing tshift, volume registration, resampling
#++ turning off deobliquing tshift, volume registration, resampling
#Script is running:
3dAttribute DELTA /Volumes/Rawr_HD/Dane/AFNI_DATA_Task1/2H_test_Jeff/TT_N27+tlrc
#Script is running:
3dAttribute DELTA /Volumes/Rawr_HD/Dane/AFNI_DATA_Task1/2H_test_Jeff/TT_N27+tlrc
#Script is running (command trimmed):
3dAttribute DELTA 2H_test_Jeff_T2_CardANATrai_SS+orig
#++ Multi-cost is lpa
#++ Removing all the temporary files
#Script is running:
rm -f __tt_TT_N27*
rm: No match.
#Script is running:
rm -f __tt_2H_test_Jeff_T2_CardANATrai_SS*
rm: No match.
#Script is running (command trimmed):
3dcopy 2H_test_Jeff_T2_CardANATrai_SS+orig __tt_2H_test_Jeff_T2_CardANATrai_SS
++ 3dcopy: AFNI version=AFNI_2011_05_26_1457 (Jul 13 2011) [64-bit]
#++ using 0th sub-brick because only one found
#Script is running (command trimmed):
3dbucket -prefix __tt_TT_N27_ts TT_N27+tlrc'[0]'
++ 3dbucket: AFNI version=AFNI_2011_05_26_1457 (Jul 13 2011) [64-bit]
#++ removing skull or area outside brain
#++ Computing weight mask
#Script is running (command trimmed):
3dBrickStat -automask -percentile 90.000000 1 90.000000 __tt_TT_N27_ts+tlrc
#++ Applying threshold of 179.000000 on /Volumes/Rawr_HD/Dane/AFNI_DATA_Task1/2H_test_Jeff/__tt_TT_N27_ts+tlrc
#Script is running (command trimmed):
3dcalc -datum float -prefix __tt_TT_N27_ts_wt -a __tt_TT_N27_ts+tlrc -expr 'min(1,(a/179.000000))'
++ 3dcalc: AFNI version=AFNI_2011_05_26_1457 (Jul 13 2011) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./__tt_TT_N27_ts_wt+tlrc.BRIK
#++ Aligning dset1 data to dset2 data
#Script is running (command trimmed):
3dAllineate -lpa -wtprefix __tt_2H_test_Jeff_T2_CardANATrai_SS_e2a_wtal -weight __tt_TT_N27_ts_wt+tlrc -source __tt_2H_test_Jeff_T2_CardANATrai_SS+orig -prefix 2H_test_Jeff_T2_CardANATrai_SS_e2a -base __tt_TT_N27_ts+tlrc -nocmass -1Dmatrix_save 2H_test_Jeff_T2_CardANATrai_SS_e2a_mat.aff12.1D -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass
++ 3dAllineate: AFNI version=AFNI_2011_05_26_1457 (Jul 13 2011) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./__tt_2H_test_Jeff_T2_CardANATrai_SS+orig.HEAD
++ Base dataset: ./__tt_TT_N27_ts+tlrc.HEAD
++ Loading datasets
++ 2214271 voxels in -source_automask+4
++ Zero-pad: not needed
++ 1440361 voxels [31.0%] in weight mask
++ Output dataset ./__tt_2H_test_Jeff_T2_CardANATrai_SS_e2a_wtal+tlrc.BRIK
++ Number of points for matching = 1440361
++ Local correlation: blok type = 'RHDD(6.54321)'
++ shift param auto-range: -51.4..51.4 -61.0..61.0 -48.2..48.2
+ Range param#4 [z-angle] = -6.000000 .. 6.000000
+ Range param#5 [x-angle] = -6.000000 .. 6.000000
+ Range param#6 [y-angle] = -6.000000 .. 6.000000
+ Range param#1 [x-shift] = -10.000000 .. 10.000000
+ Range param#2 [y-shift] = -10.000000 .. 10.000000
+ Range param#3 [z-shift] = -10.000000 .. 10.000000
+ 12 free parameters
++ Normalized convergence radius = 0.001000
++ OpenMP thread count = 16
++ ======= Allineation of 1 sub-bricks using Local Pearson Correlation Abs =======
++ ========== sub-brick #0 ========== [total CPU to here=10.6 s]
++ *** Fine pass begins ***
+ * Enter alignment setup routine
+ - copying base image
+ - copying source image
+ - copying weight image
+ - using 1440361 points from base image [use_all=0]
+ * Exit alignment setup routine
+ 1366946 total points stored in 2584 'RHDD(6.54321)' bloks
+ - Initial cost = 0.988782
+ - Initial fine Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000
***************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
+ - Finalish cost = 0.983916 ; 794 funcs
*****
+ - Final cost = 0.983915 ; 120 funcs
+ Final fine fit Parameters = 0.0779 -1.9439 2.4112 0.7996 0.1523 1.7112 1.0203 1.0195 0.9731 0.0030 0.0129 -0.0148
+ - Fine net CPU time = 112.1 s
++ Computing output image
++ image warp: parameters = 0.0779 -1.9439 2.4112 0.7996 0.1523 1.7112 1.0203 1.0195 0.9731 0.0030 0.0129 -0.0148
++ Wrote -1Dmatrix_save 2H_test_Jeff_T2_CardANATrai_SS_e2a_mat.aff12.1D
++ total CPU time = 127.1 sec Elapsed = 40.3
++ ###########################################################
++ ### Please check results visually for alignment quality ###
++ ###########################################################
#Script is running:
rm -f AddEdge/*
#++ resampling dset2 to match dset1 data
#Script is running (command trimmed):
3dresample -master __tt_2H_test_Jeff_T2_CardANATrai_SS+orig -prefix __tt_TT_N27_rs_in -inset __tt_TT_N27_ts+tlrc'' -rmode Cu
** ERROR: Could not resample

Traceback (most recent call last):
File "/abin/align_epi_anat.py", line 3105, in <module>
listlog = listlog_a2e)
File "/abin/align_epi_anat.py", line 2617, in add_edges
d1AE = d1.new("%s" % d1name)
AttributeError: 'NoneType' object has no attribute 'new'
mv: rename 2H_test_Jeff_anat_brain_e2a_mat.aff12.1D to AddEdge/2H_test_Jeff_anat_brain_e2a_mat.aff12.1D: No such file or directory
mv: rename 2H_test_Jeff_vr_z4_e2a_mat.aff12.1D to AddEdge/2H_test_Jeff_vr_z4_e2a_mat.aff12.1D: No such file or directory
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