Hello,
Based on AFNI message board recommendations, I am attempting to tlrc my anatomical data to MNI template (2009c version) using auto_warp. I have successfully completed this in the GUI using the “@auto_tlrc” option, but when I try to use “auto_warp” in the GUI I receive the following error:
cat_matvec 10404.anat_ns+tlrc::WARP_DATA -I
e ERROR:e[0m THD_read_dvecmat: can’t open dataset 10404.anat_ns+tlrc
e[7m** FATAL ERROR:e[0m Can’t read matrix from ‘10404.anat_ns+tlrc::WARP_DATA’
** Program compile date = Apr 30 2018[7m**
My pre-processing script for this part is:
warp anatomy to standard space
auto_warp.py -base MNI152_T1_2009c+tlrc -input 10404.anat_ns+orig
I looked at the output (see below), and it seems that my XXX.anat_ns+tlrc is not being created. Is it possible to run the auto_warp in the GUI created pre-processing script?
Thank you so much in advance for your help.
Best,
Tamara
Output:
echo auto-generated by afni_proc.py, Fri Jul 6 15:14:31 2018
auto-generated by afni_proc.py, Fri Jul 6 15:14:31 2018
echo (version 6.10, Apr 26, 2018)
(version 6.10, Apr 26, 2018)
echo execution started: date
date
execution started: Fri Jul 6 16:06:22 EDT 2018
afni -ver
Precompiled binary linux_ubuntu_16_64: Apr 30 2018 (Version AFNI_18.1.09)
afni_history -check_date 23 Mar 2018
– is current: afni_history as new as: 23 Mar 2018
most recent entry is: 29 Apr 2018
if ( 0 ) then
if ( 0 > 0 ) then
set subj = s_10404
endif
set output_dir = s_10404.results
if ( -d s_10404.results ) then
set runs = ( count -digits 2 1 4 )
count -digits 2 1 4
mkdir s_10404.results
mkdir s_10404.results/stimuli
cp /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/NonRevP_learn_corr_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/NonRevP_learn_corr.txt /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/NonRevP_learn_incor_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/NonRevP_learn_incor.txt /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/NonRevP_perf_corr_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/NonRevP_perf_corr.txt /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/NonRevP_perf_incor_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/NonRevP_perf_incor.txt /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/RevP_acq_corr_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/RevP_acq_corr.txt /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/RevP_acq_incor_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/RevP_acq_incor.txt /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/RevP_rev_corr_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/RevP_rev_corr.txt /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/RevP_rev_incor_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/RevP_rev_incor.txt s_10404.results/stimuli
3dcopy /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/10404.anat+orig s_10404.results/10404.anat
++ 3dcopy: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
3dTcat -prefix s_10404.results/pb00.s_10404.r01.tcat /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/10404.1+orig[0…$]
++ 3dTcat: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ elapsed time = 0.4 s
3dTcat -prefix s_10404.results/pb00.s_10404.r02.tcat /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/10404.2+orig[0…$]
++ 3dTcat: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ elapsed time = 0.4 s
3dTcat -prefix s_10404.results/pb00.s_10404.r03.tcat /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/10404.3+orig[0…$]
++ 3dTcat: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ elapsed time = 0.4 s
3dTcat -prefix s_10404.results/pb00.s_10404.r04.tcat /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/10404.4+orig[0…$]
++ 3dTcat: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ elapsed time = 0.4 s
set tr_counts = ( 153 153 153 153 )
cd s_10404.results
touch out.pre_ss_warn.txt
foreach run ( 01 02 03 04 )
3dToutcount -automask -fraction -polort 3 -legendre pb00.s_10404.r01.tcat+orig
++ 3dToutcount: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
e[7m*+ WARNING:e[0m If you are performing spatial transformations on an oblique dset,
such as ./pb00.s_10404.r01.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.s_10404.r01.tcat+orig.BRIK is 20.008726 degrees from plumb.
++ 97958 voxels passed mask/clip
if ( 1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)" ) then
1deval -a outcount.r01.1D{0} -expr step(a-0.4)
end
3dToutcount -automask -fraction -polort 3 -legendre pb00.s_10404.r02.tcat+orig
++ 3dToutcount: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
e[7m*+ WARNING:e[0m If you are performing spatial transformations on an oblique dset,
such as ./pb00.s_10404.r02.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.s_10404.r02.tcat+orig.BRIK is 20.008726 degrees from plumb.
++ 98001 voxels passed mask/clip
if ( 1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)" ) then
1deval -a outcount.r02.1D{0} -expr step(a-0.4)
end
3dToutcount -automask -fraction -polort 3 -legendre pb00.s_10404.r03.tcat+orig
++ 3dToutcount: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
e[7m*+ WARNING:e[0m If you are performing spatial transformations on an oblique dset,
such as ./pb00.s_10404.r03.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.s_10404.r03.tcat+orig.BRIK is 20.008726 degrees from plumb.
++ 97767 voxels passed mask/clip
if ( 1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)" ) then
1deval -a outcount.r03.1D{0} -expr step(a-0.4)
end
3dToutcount -automask -fraction -polort 3 -legendre pb00.s_10404.r04.tcat+orig
++ 3dToutcount: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
e[7m*+ WARNING:e[0m If you are performing spatial transformations on an oblique dset,
such as ./pb00.s_10404.r04.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.s_10404.r04.tcat+orig.BRIK is 20.008726 degrees from plumb.
++ 98095 voxels passed mask/clip
if ( 1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)" ) then
1deval -a outcount.r04.1D{0} -expr step(a-0.4)
end
cat outcount.r01.1D outcount.r02.1D outcount.r03.1D outcount.r04.1D
set minindex = 3dTstat -argmin -prefix - outcount_rall.1D\'
3dTstat -argmin -prefix - outcount_rall.1D’
++ 3dTstat: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: KR Hammett & RW Cox
e[7m*+ WARNING:e[0m Input dataset is not 3D+time; assuming TR=1.0
set ovals = ( 1d_tool.py -set_run_lengths $tr_counts -index_to_run_tr $minindex )
1d_tool.py -set_run_lengths 153 153 153 153 -index_to_run_tr 499
set minoutrun = 04
set minouttr = 40
echo min outlier: run 04, TR 40
tee out.min_outlier.txt
min outlier: run 04, TR 40
foreach run ( 01 02 03 04 )
3dTshift -tzero 0 -quintic -prefix pb01.s_10404.r01.tshift pb00.s_10404.r01.tcat+orig
++ 3dTshift: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
e[7m*+ WARNING:e[0m If you are performing spatial transformations on an oblique dset,
such as ./pb00.s_10404.r01.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.s_10404.r01.tcat+orig.BRIK is 20.008726 degrees from plumb.
end
3dTshift -tzero 0 -quintic -prefix pb01.s_10404.r02.tshift pb00.s_10404.r02.tcat+orig
++ 3dTshift: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
e[7m*+ WARNING:e[0m If you are performing spatial transformations on an oblique dset,
such as ./pb00.s_10404.r02.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.s_10404.r02.tcat+orig.BRIK is 20.008726 degrees from plumb.
end
3dTshift -tzero 0 -quintic -prefix pb01.s_10404.r03.tshift pb00.s_10404.r03.tcat+orig
++ 3dTshift: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
e[7m*+ WARNING:e[0m If you are performing spatial transformations on an oblique dset,
such as ./pb00.s_10404.r03.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.s_10404.r03.tcat+orig.BRIK is 20.008726 degrees from plumb.
end
3dTshift -tzero 0 -quintic -prefix pb01.s_10404.r04.tshift pb00.s_10404.r04.tcat+orig
++ 3dTshift: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
e[7m*+ WARNING:e[0m If you are performing spatial transformations on an oblique dset,
such as ./pb00.s_10404.r04.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.s_10404.r04.tcat+orig.BRIK is 20.008726 degrees from plumb.
end
3dbucket -prefix vr_base_min_outlier pb01.s_10404.r04.tshift+orig[40]
++ 3dbucket: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
align_epi_anat.py -anat2epi -anat 10404.anat+orig -save_skullstrip -suffix _al_junk -epi vr_base_min_outlier+orig -epi_base 0 -epi_strip 3dAutomask -volreg off -tshift off
#++ align_epi_anat version: 1.58
#++ turning off volume registration
#Script is running (command trimmed):
3dAttribute DELTA ./vr_base_min_outlier+orig
#Script is running (command trimmed):
3dAttribute DELTA ./vr_base_min_outlier+orig
#Script is running (command trimmed):
3dAttribute DELTA ./10404.anat+orig
#++ Multi-cost is lpc
#++ Removing all the temporary files
#Script is running:
\rm -f ./__tt_vr_base_min_outlier*
#Script is running:
\rm -f ./__tt_10404.anat*
#Script is running (command trimmed):
3dcopy ./10404.anat+orig ./__tt_10404.anat+orig
++ 3dcopy: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
#++ Removing skull from anat data
#Script is running (command trimmed):
3dSkullStrip -orig_vol -input ./__tt_10404.anat+orig -prefix ./__tt_10404.anat_ns
e[7m*+ WARNING:e[0m If you are performing spatial transformations on an oblique dset,
such as ./__tt_10404.anat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./__tt_10404.anat+orig.BRIK is 0.142653 degrees from plumb.
#Script is running (command trimmed):
3dinfo ./__tt_10404.anat_ns+orig | \grep ‘Data Axes Tilt:’|\grep ‘Oblique’
#++ Dataset /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/s_10404.results/__tt_10404.anat_ns+orig is oblique*
#Script is running (command trimmed):
3dAttribute DELTA ./__tt_10404.anat_ns+orig
#++ Spacing for anat to oblique epi alignment is 1.000000
#++ Matching obliquity of anat to epi
#Script is running (command trimmed):
3dWarp -verb -card2oblique ./vr_base_min_outlier+orig -prefix ./__tt_10404.anat_ns_ob -newgrid 1.000000 ./__tt_10404.anat_ns+orig | \grep -A 4 ‘# mat44 Obliquity Transformation ::’ > ./__tt_10404.anat_ns_obla2e_mat.1D
++ 3dWarp: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: RW Cox
++ Deobliquing original dataset before obliquing
++ Combining oblique transformations
#++ using 0th sub-brick because only one found
#Script is running (command trimmed):
3dbucket -prefix ./__tt_vr_base_min_outlier_ts ./vr_base_min_outlier+orig’[0]’
++ 3dbucket: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
#++ resampling epi to match anat data
#Script is running (command trimmed):
3dresample -master ./__tt_10404.anat_ns_ob+orig -prefix ./__tt_vr_base_min_outlier_ts_rs -inset ./__tt_vr_base_min_outlier_ts+orig’’ -rmode Cu
e[7m*+ WARNING:e[0m If you are performing spatial transformations on an oblique dset,
such as ./__tt_vr_base_min_outlier_ts+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./__tt_vr_base_min_outlier_ts+orig.BRIK is 20.008726 degrees from plumb.
#++ removing skull or area outside brain
#Script is running (command trimmed):
3dAutomask -apply_prefix ./__tt_vr_base_min_outlier_ts_rs_ns ./__tt_vr_base_min_outlier_ts_rs+orig
++ 3dAutomask: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset ./__tt_vr_base_min_outlier_ts_rs+orig
++ Forming automask
- Fixed clip level = 189.040802
- Used gradual clip level = 178.500000 … 205.497604
- Number voxels above clip level = 1186097
- Clustering voxels …
- Largest cluster has 1168084 voxels
- Clustering voxels …
- Largest cluster has 1166553 voxels
- Filled 2016 voxels in small holes; now have 1168569 voxels
- Filled 40740 voxels in large holes; now have 1209309 voxels
- Clustering voxels …
- Largest cluster has 1209301 voxels
- Clustering non-brain voxels …
- Clustering voxels …
- Largest cluster has 18792499 voxels
- Mask now has 1209301 voxels
++ 1209301 voxels in the mask [out of 20001800: 6.05%]
++ first 28 x-planes are zero [from R]
++ last 32 x-planes are zero [from L]
++ first 100 y-planes are zero [from A]
++ last 57 y-planes are zero [from P]
++ first 127 z-planes are zero [from I]
++ last 87 z-planes are zero [from S]
++ applying mask to original data
++ Writing masked data
++ CPU time = 0.000000 sec
#++ Computing weight mask
#Script is running (command trimmed):
3dBrickStat -automask -percentile 90.000000 1 90.000000 ./__tt_vr_base_min_outlier_ts_rs_ns+orig
#++ Applying threshold of 506.000000 on /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/s_10404.results/__tt_vr_base_min_outlier_ts_rs_ns+orig
#Script is running (command trimmed):
3dcalc -datum float -prefix ./__tt_vr_base_min_outlier_ts_rs_ns_wt -a ./__tt_vr_base_min_outlier_ts_rs_ns+orig -expr ‘min(1,(a/506.000000))’
++ 3dcalc: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: A cast of thousands
#++ Aligning anat data to epi data
#Script is running (command trimmed):
3dAllineate -lpc -wtprefix ./__tt_10404.anat_ns_ob_al_junk_wtal -weight ./__tt_vr_base_min_outlier_ts_rs_ns_wt+orig -source ./__tt_10404.anat_ns_ob+orig -prefix ./__tt_10404.anat_ns_ob_temp_al_junk -base ./__tt_vr_base_min_outlier_ts_rs_ns+orig -nocmass -1Dmatrix_save ./10404.anat_al_junk_e2a_only_mat.aff12.1D -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass
++ 3dAllineate: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./__tt_10404.anat_ns_ob+orig.HEAD
++ Base dataset: ./__tt_vr_base_min_outlier_ts_rs_ns+orig.HEAD
++ Loading datasets
++ 1542615 voxels in -source_automask+4
++ Zero-pad: not needed
++ 1209289 voxels [6.0%] in weight mask
++ Number of points for matching = 1209289
++ Local correlation: blok type = ‘RHDD(6.54321)’
++ shift param auto-range: -62.6…62.6 -100.5…100.5 -104.0…104.0 - 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 = 8
++ ======= Allineation of 1 sub-bricks using Local Pearson Correlation Signed =======
++ ========== sub-brick #0 ========== [total CPU to here=0.0 s]
++ *** Fine pass begins *** -
- Enter alignment setup routine
-
- copying base image
-
- copying source image
-
- copying weight image
-
- using 1209289 points from base image [use_all=0]
-
- Exit alignment setup routine
- 1140635 total points stored in 2132 ‘RHDD(6.54321)’ bloks
-
- Initial cost = -0.443807
-
- 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 = -0.863472 ; 284 funcs
-
- Final cost = -0.863485 ; 102 funcs
- Final fine fit Parameters:
x-shift= 0.0622 y-shift=-0.0170 z-shift=-0.5965
z-angle= 0.3222 x-angle= 1.2645 y-angle=-0.0023
x-scale= 1.0001 y-scale= 1.0082 z-scale= 0.9962
y/x-shear=-0.0053 z/x-shear=-0.0001 z/y-shear=-0.0049 -
- Fine net CPU time = 0.0 s
++ Computing output image
++ image warp: parameters = 0.0622 -0.0170 -0.5965 0.3222 1.2645 -0.0023 1.0001 1.0082 0.9962 -0.0053 -0.0001 -0.0049
++ Wrote -1Dmatrix_save ./10404.anat_al_junk_e2a_only_mat.aff12.1D
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 75.5
++ ###########################################################
++ # Please check results visually for alignment quality #
++ ###########################################################
++ # ‘-autoweight’ is recommended when using -lpc or -lpa #
++ # If your results are not good, please try again. #
++ ###########################################################
#Script is running (command trimmed):
cat_matvec -ONELINE ./10404.anat_al_junk_e2a_only_mat.aff12.1D ./__tt_10404.anat_ns_obla2e_mat.1D -I > ./10404.anat_al_junk_mat.aff12.1D
#++ Combining anat to epi and oblique transformations
#Script is running (command trimmed):
3dAllineate -base ./__tt_vr_base_min_outlier_ts_rs_ns+orig -1Dmatrix_apply ./10404.anat_al_junk_mat.aff12.1D -prefix ./10404.anat_al_junk -input ./__tt_10404.anat_ns+orig -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass
++ 3dAllineate: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Zhark the Registrator
e[7m*+ WARNING:e[0m If you are performing spatial transformations on an oblique dset,
such as ./__tt_10404.anat_ns+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./__tt_10404.anat_ns+orig.BRIK is 0.142653 degrees from plumb.
++ Source dataset: ./__tt_10404.anat_ns+orig.HEAD
++ Base dataset: ./__tt_vr_base_min_outlier_ts_rs_ns+orig.HEAD
++ Loading datasets
++ NOTE: base and source coordinate systems have different handedness
- Fine net CPU time = 0.0 s
-
Orientations: base=Right handed (RAI); source=Left handed (ASR) - 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
++ OpenMP thread count = 8
++ ========== Applying transformation to 1 sub-bricks ==========
++ ========== 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 = 0.9380 -0.3615 -0.0121 16.4626 0.3701 0.9282 0.0078 -52.4049 0.0030 -0.0115 1.0001 1.0392
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 2.5
++ ###########################################################
#++ Creating final output: skullstripped anat data
copying from dataset /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/s_10404.results/__tt_10404.anat_ns+orig to /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/s_10404.results/10404.anat_ns+orig
#Script is running (command trimmed):
3dcopy ./__tt_10404.anat_ns+orig 10404.anat_ns
++ 3dcopy: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
#++ Creating final output: anat data aligned to epi
- Exit alignment setup routine
copy is not necessary
#++ Saving history
#Script is running (command trimmed):
3dNotes -h “align_epi_anat.py -anat2epi -anat 10404.anat+orig
-save_skullstrip -suffix _al_junk -epi vr_base_min_outlier+orig -epi_base
0 -epi_strip 3dAutomask -volreg off -tshift off”
./10404.anat_al_junk+orig
#++ Removing all the temporary files
#Script is running:
\rm -f ./__tt_vr_base_min_outlier*
#Script is running:
\rm -f ./__tt_10404.anat*
Finished alignment successfully
auto_warp.py -base MNI152_T1_2009c+tlrc -input 10404.anat_ns+orig
#++ auto_warp.py version: 0.04
Output directory /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/s_10404.results/awpy/
#Script is running (command trimmed):
mkdir ./awpy/
cd /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/s_10404.results/awpy/
#Script is running (command trimmed):
3dcopy /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/s_10404.results/10404.anat_ns+orig ./anat.nii
++ 3dcopy: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
#Script is running (command trimmed):
3dUnifize -GM -input ./anat.nii -prefix ./anat.un.nii
++ 3dUnifize: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
e[7m*+ WARNING:e[0m If you are performing spatial transformations on an oblique dset,
such as ./anat.nii,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./anat.nii is 0.142653 degrees from plumb.
- Pre-processing: ADV…UWG
++ Output dataset ./anat.un.nii
++ ===== Elapsed = 16.1 sec
#Script is running (command trimmed):
3dcopy /home/bmiadmin/abin/MNI152_T1_2009c+tlrc ./base.nii
++ 3dcopy: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
#++ Aligning /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/s_10404.results/awpy/base.nii data to /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/s_10404.results/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_18.1.09 (Apr 30 2018) [64-bit]
e[7m*+ WARNING:e[0m If you are performing spatial transformations on an oblique dset,
such as ./anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA+orig.BRIK is 0.142653 degrees from plumb.
Performing center alignment with @Align_Centers
e[7m*+ WARNING:e[0m If you are performing spatial transformations on an oblique dset,
such as ./anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA+orig.BRIK is 0.142653 degrees from plumb.
++ 3dcopy: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ 3drefit: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset ./anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig
- deoblique
++ 3drefit processed 1 datasets
++ 3drename: AFNI version=AFNI_18.1.09 (Apr 30 2018) [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_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: RW Cox
e[7m*+ WARNING:e[0m If you are performing spatial transformations on an oblique dset,
such as ./anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA+orig.BRIK is 0.142653 degrees from plumb.
++ 0.142653 degrees from plumb.
e[7m*+ WARNING:e[0m Deoblique datasets with 3dWarp before proceeding with other transformations
Center distance of 0.000065 mm
Padding …
++ 3dZeropad: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ output dataset: ./__ats_tmp__ref_base.nii_40pad+tlrc.BRIK
Resampling …
++ 3dcalc: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: A cast of thousands
++ 3dcalc: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: A cast of thousands
Clipping -0.000100 3145.580100 …
++ 3dcalc: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: A cast of thousands
++ 3drefit: AFNI version=AFNI_18.1.09 (Apr 30 2018) [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_18.1.09 (Apr 30 2018) [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_18.1.09 (Apr 30 2018) [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_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: RW Cox
RMS[0] = 123.451 69.5635 ITER = 12/137
123.451
Warping has converged.
++ 3dcopy: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ 3dWarp: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: RW Cox
e[7m*+ WARNING:e[0m If you are performing spatial transformations on an oblique dset,
such as ./anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA+orig.BRIK is 0.142653 degrees from plumb.
++ 0.142653 degrees from plumb.
e[7m*+ WARNING:e[0m Deoblique datasets with 3dWarp before proceeding with other transformations
Applying brain mask
++ 3dcalc: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: A cast of thousands
++ 3dWarp: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: RW Cox
++ 3drename: AFNI version=AFNI_18.1.09 (Apr 30 2018) [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_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: A cast of thousands
Unpadding …
++ 3dZeropad: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ output dataset: ./__ats_tmp___upad40_pre.anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA.aff+orig.BRIK
++ 3drefit: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp___upad40_pre.anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA.aff+orig
e[7m*+ WARNING:e[0m Changing the space of an ORIG view dataset may cause confusion!
e[7m*+ WARNING:e[0m NIFTI copies will be interpreted as TLRC view (not TLRC space).
e[7m*+ WARNING:e[0m Consider changing the view of the dataset to TLRC view also
++ 3drefit processed 1 datasets
Changing view of transformed anatomy
++ 3drefit: AFNI version=AFNI_18.1.09 (Apr 30 2018) [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_18.1.09 (Apr 30 2018) [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_18.1.09 (Apr 30 2018) [64-bit]
Cleanup …
++ 3drename: AFNI version=AFNI_18.1.09 (Apr 30 2018) [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_18.1.09 (Apr 30 2018) [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 (command trimmed):
3dAttribute DELTA ./anat.un.aff.nii
#Script is running (command trimmed):
3dAttribute DELTA ./base.nii
1.000000 1.000000
#Script is running (command trimmed):
3dinfo -same_grid ./anat.un.aff.nii ./base.nii
#++ Aligning /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/s_10404.results/awpy/base.nii data to /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/s_10404.results/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 = 8
++ 3dQwarp: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
++ Dataset zero-pad: xbot=0 xtop=0 ybot=1 ytop=2 zbot=15 ztop=0 voxels
++ Weightizing the base image
++ +++++++++++ Begin warp optimization: base=./base.nii source=./anat.un.aff.nii
++ AFNI warpomatic: 193 x 232 x 208 volume ; autobbox = 19…173 21…211 17…179 [clock= 9s 163ms]
lev=0 0…192 0…231 0…199: [first cost=-0.39929] … done [cost:-0.39929==>-0.56500]
lev=1 patch=145x175x157 [clock= 15m 44s 147ms]…:[cost=-0.59915]:… done [cost:-0.56500==>-0.60587 ; 16 patches optimized, 0 skipped]
lev=2 patch=109x131x117 [clock= 31m 31s 363ms]… done [cost:-0.60587==>-0.65417 ; 21 patches optimized, 6 skipped]
lev=3 patch=81x99x89 [clock= 42m 12s 501ms]… done [cost:-0.65417==>-0.71209 ; 41 patches optimized, 23 skipped]
lev=4 patch=61x73x67 [clock= 53m 37s 760ms]… done [cost:-0.71209==>-0.73319 ; 73 patches optimized, 52 skipped]
lev=5 patch=47x55x49 [clock= 1h 7m 23s 360ms]… done [cost:-0.73319==>-0.82525 ; 193 patches optimized, 150 skipped]
lev=6 patch=35x41x37 [clock= 1h 24m 57s 830ms]… done [cost:-0.82525==>-0.85644 ; 451 patches optimized, 359 skipped]
lev=7 patch=25x25x25 [clock= 1h 54m 46s 820ms]… done [cost:-0.85644==>-0.92589 ; 1528 patches optimized, 1384 skipped]
++ ========== total number of parameters ‘optimized’ = 56049
++ Output dataset ./anat.un.aff.qw.nii
++ Output dataset ./anat.un.aff.qw_WARP.nii
++ ===== clock time = 3h 7m 6s 547ms
#++ Applying warps to /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/s_10404.results/10404.anat_ns+orig
#Script is running (command trimmed):
3dNwarpApply -nwarp “./anat.un.aff.qw_WARP.nii anat.un.aff.Xat.1D” -master ./base.nii -source /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/s_10404.results/10404.anat_ns+orig -prefix ./10404.anat_ns.aw.nii
++ 3dNwarpApply: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Zhark the Warped
++ -master dataset is ‘./base.nii’
e[7m*+ WARNING:e[0m If you are performing spatial transformations on an oblique dset,
such as /home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/s_10404.results/10404.anat_ns+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:/home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/s_10404.results/10404.anat_ns+orig.BRIK is 0.142653 degrees from plumb.
++ opened source dataset ‘/home/bmiadmin/Tamara/PRR_Analysis/Test_analysis/Manual_tlrc_July6_2018/MNI_auto_manual/Auto/10404_autoWarp/s_10404.results/10404.anat_ns+orig’
++ Processing -nwarp
++ Warping:.Z
++ Output dataset ./10404.anat_ns.aw.nii
++ total Elapsed time = 7.8 sec
#++ Saving history
#Script is running (command trimmed):
3dNotes -h “auto_warp.py -base MNI152_T1_2009c+tlrc -input
10404.anat_ns+orig”
./10404.anat_ns.aw.nii
cat_matvec 10404.anat_ns+tlrc::WARP_DATA -I
e ERROR:e[0m THD_read_dvecmat: can’t open dataset 10404.anat_ns+tlrc
e[7m** FATAL ERROR:e[0m Can’t read matrix from ‘10404.anat_ns+tlrc::WARP_DATA’
** Program compile date = Apr 30 2018[7m**