Hello everyone,
I’m new to AFNI and am having trouble running my single subject processing script. I’m using uber_subject.py and get a few errors, including the following fatal error:
*+ WARNING: input ‘a’ is not used in the expression
++ Output dataset ./rm.epi.all1+orig.BRIK
cat_matvec -ONELINE obl_s0114.mprage_ns+tlrc::WARP_DATA -I obl_s0114.mprage_al_junk_mat.aff12.1D -I mat.r01.vr.aff12.1D
** FATAL ERROR: Can’t read file ‘obl_s0114.mprage_al_junk_mat.aff12.1D’
Any help is greatly appreciated. Note that this al_junk_mat.aff12.1D file isn’t showing up in my results directory. Also, here is the full output in case that is more helpful:
echo auto-generated by afni_proc.py, Mon Nov 7 14:27:32 2016
auto-generated by afni_proc.py, Mon Nov 7 14:27:32 2016
echo (version 5.08, October 20, 2016)
(version 5.08, October 20, 2016)
echo execution started: date
date
execution started: Mon Nov 7 14:28:31 PST 2016
afni -ver
Precompiled binary macosx_10.7_Intel_64: Oct 24 2016 (Version AFNI_16.3.05)
afni_history -check_date 23 Sep 2016
– is current: afni_history as new as: 23 Sep 2016
most recent entry is: 20 Oct 2016
if ( 0 ) then
if ( 0 > 0 ) then
set subj = s0114
endif
set output_dir = s0114.results
if ( -d s0114.results ) then
set runs = ( count -digits 2 1 2 )
count -digits 2 1 2
mkdir s0114.results
mkdir s0114.results/stimuli
cp /Users/jgemilleadmin/Desktop/DissData/s1901/Dir_ToM/Belief.1D /Users/jgemilleadmin/Desktop/DissData/s1901/Dir_ToM/Photo.1D s0114.results/stimuli
3dcopy /Users/jgemilleadmin/Desktop/DissData/s0114/obl_s0114.mprage.nii s0114.results/obl_s0114.mprage
++ 3dcopy: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
3dTcat -prefix s0114.results/pb00.s0114.r01.tcat /Users/jgemilleadmin/Desktop/DissData/s0114/obl_s0114.ToMrun01.nii[0…$]
++ 3dTcat: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
++ elapsed time = 0.3 s
3dTcat -prefix s0114.results/pb00.s0114.r02.tcat /Users/jgemilleadmin/Desktop/DissData/s0114/obl_s0114.ToMrun02.nii[0…$]
++ 3dTcat: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
++ elapsed time = 0.3 s
set tr_counts = ( 138 138 )
cd s0114.results
touch out.pre_ss_warn.txt
foreach run ( 01 02 )
3dToutcount -automask -fraction -polort 2 -legendre pb00.s0114.r01.tcat+orig
++ 3dToutcount: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
++ 37194 voxels passed mask/clip
1deval -a outcount.r01.1D -expr 1-step(a-0.1)
if ( 1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)" ) then
1deval -a outcount.r01.1D{0} -expr step(a-0.4)
end
3dToutcount -automask -fraction -polort 2 -legendre pb00.s0114.r02.tcat+orig
++ 3dToutcount: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
++ 37315 voxels passed mask/clip
1deval -a outcount.r02.1D -expr 1-step(a-0.1)
if ( 1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)" ) then
1deval -a outcount.r02.1D{0} -expr step(a-0.4)
end
cat outcount.r01.1D outcount.r02.1D
cat rm.out.cen.r01.1D rm.out.cen.r02.1D
foreach run ( 01 02 )
3dTshift -tzero 0 -quintic -prefix pb01.s0114.r01.tshift pb00.s0114.r01.tcat+orig
++ 3dTshift: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
*+ WARNING: dataset is already aligned in time!
*+ WARNING: ==>> output dataset is just a copy of input dataset
end
3dTshift -tzero 0 -quintic -prefix pb01.s0114.r02.tshift pb00.s0114.r02.tcat+orig
++ 3dTshift: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
+ WARNING: dataset is already aligned in time!
+ WARNING: ==>> output dataset is just a copy of input dataset
end
3dbucket -prefix vr_base pb01.s0114.r01.tshift+orig[0]
++ 3dbucket: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
align_epi_anat.py -anat2epi -anat obl_s0114.mprage+orig -save_skullstrip -suffix _al_junk -epi vr_base+orig -epi_base 0 -epi_strip 3dAutomask -volreg off -tshift off
#++ align_epi_anat version: 1.55
#++ turning off volume registration
#Script is running (command trimmed):
3dAttribute DELTA ./vr_base+orig
#Script is running (command trimmed):
3dAttribute DELTA ./vr_base+orig
#Script is running (command trimmed):
3dAttribute DELTA ./obl_s0114.mprage+orig
#++ Multi-cost is lpc
#++ Removing all the temporary files
#Script is running:
\rm -f ./__tt_vr_base
#Script is running:
\rm -f ./__tt_obl_s0114.mprage
#Script is running (command trimmed):
3dcopy ./obl_s0114.mprage+orig ./__tt_obl_s0114.mprage+orig
++ 3dcopy: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
#++ Removing skull from anat data
#Script is running (command trimmed):
3dSkullStrip -orig_vol -input ./__tt_obl_s0114.mprage+orig -prefix ./__tt_obl_s0114.mprage_ns
#Script is running (command trimmed):
3dinfo ./__tt_obl_s0114.mprage_ns+orig | \grep ‘Data Axes Tilt:’|\grep ‘Oblique’
#++ Dataset /Users/jgemilleadmin/Desktop/DissData/s0114/subject_results/group.g002/subj.s0114/s0114.results/__tt_obl_s0114.mprage_ns+orig is not oblique
#Script is running (command trimmed):
3dinfo ./vr_base+orig | \grep ‘Data Axes Tilt:’|\grep ‘Oblique’
#++ Dataset /Users/jgemilleadmin/Desktop/DissData/s0114/subject_results/group.g002/subj.s0114/s0114.results/vr_base+orig is not oblique
#++ using 0th sub-brick because only one found
#Script is running (command trimmed):
3dbucket -prefix ./__tt_vr_base_ts ./vr_base+orig’[0]’
++ 3dbucket: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
#++ resampling epi to match anat data
#Script is running (command trimmed):
3dresample -master ./__tt_obl_s0114.mprage_ns+orig -prefix ./__tt_vr_base_ts_rs -inset ./__tt_vr_base_ts+orig’’ -rmode Cu
#++ removing skull or area outside brain
#Script is running (command trimmed):
3dAutomask -apply_prefix ./__tt_vr_base_ts_rs_ns ./__tt_vr_base_ts_rs+orig
++ 3dAutomask: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset ./__tt_vr_base_ts_rs+orig
++ Forming automask
- Fixed clip level = 325.039886
- Used gradual clip level = 257.045410 … 460.969391
- Number voxels above clip level = 1863917
- Clustering voxels …
- Largest cluster has 1854812 voxels
- Clustering voxels …
- Largest cluster has 1853049 voxels
- Filled 1203 voxels in small holes; now have 1854252 voxels
- Filled 49036 voxels in large holes; now have 1903288 voxels
- Clustering voxels …
- Largest cluster has 1903195 voxels
- Clustering non-brain voxels …
- Clustering voxels …
- Largest cluster has 11847333 voxels
- Mask now has 1903195 voxels
++ 1903195 voxels in the mask [out of 13750528: 13.84%]
++ first 22 x-planes are zero [from R]
++ last 20 x-planes are zero [from L]
++ first 41 y-planes are zero [from A]
++ last 22 y-planes are zero [from P]
++ first 97 z-planes are zero [from I]
++ last 23 z-planes are zero [from S]
++ applying mask to original data
++ Writing masked data
++ Output dataset ./__tt_vr_base_ts_rs_ns+orig.BRIK
++ CPU time = 3.440000 sec
#++ Computing weight mask
#Script is running (command trimmed):
3dBrickStat -automask -percentile 90.000000 1 90.000000 ./__tt_vr_base_ts_rs_ns+orig
#++ Applying threshold of 1026.000000 on /Users/jgemilleadmin/Desktop/DissData/s0114/subject_results/group.g002/subj.s0114/s0114.results/__tt_vr_base_ts_rs_ns+orig
#Script is running (command trimmed):
3dcalc -datum float -prefix ./__tt_vr_base_ts_rs_ns_wt -a ./__tt_vr_base_ts_rs_ns+orig -expr ‘min(1,(a/1026.000000))’
++ 3dcalc: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tt_vr_base_ts_rs_ns_wt+orig.BRIK
#++ Aligning anat data to epi data
#Script is running (command trimmed):
3dAllineate -lpc -wtprefix ./__tt_obl_s0114.mprage_ns_al_junk_wtal -weight ./__tt_vr_base_ts_rs_ns_wt+orig -source ./__tt_obl_s0114.mprage_ns+orig -prefix ./obl_s0114.mprage_al_junk -base ./__tt_vr_base_ts_rs_ns+orig -nocmass -1Dmatrix_save ./obl_s0114.mprage_al_junk_mat.aff12.1D -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass
dyld: Library not loaded: /usr/local/lib/libgomp.1.dylib
Referenced from: /Users/jgemilleadmin/abin/3dAllineate
Reason: image not found
#++ Creating final output: skullstripped anat data
#Script is running (command trimmed):
3dcopy ./__tt_obl_s0114.mprage_ns+orig obl_s0114.mprage_ns
++ 3dcopy: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
#++ Creating final output: anat data aligned to epi
copy is not necessary
#++ Saving history
#Script is running (command trimmed):
3dNotes -h “align_epi_anat.py -anat2epi -anat obl_s0114.mprage+orig
-save_skullstrip -suffix _al_junk -epi vr_base+orig -epi_base 0
-epi_strip 3dAutomask -volreg off -tshift off”
./obl_s0114.mprage_al_junk+orig
Error: Cannot open dataset
#++ Removing all the temporary files
#Script is running:
\rm -f ./__tt_vr_base*
#Script is running:
\rm -f ./__tt_obl_s0114.mprage*
Finished alignment successfully
@auto_tlrc -base MNI_avg152T1+tlrc -input obl_s0114.mprage_ns+orig -no_ss -init_xform AUTO_CENTER
Performing center alignment with @Align_Centers
++ 3dcopy: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
++ 3drefit: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset ./obl_s0114.mprage_ns_shft+orig
++ 3drefit processed 1 datasets
++ 3drename: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
++ THD_rename_dataset_files: rename obl_s0114.mprage_ns_shft+orig.HEAD → __ats_tmp__obl_s0114.mprage_ns_shft+orig.HEAD
++ THD_rename_dataset_files: rename obl_s0114.mprage_ns_shft+orig.BRIK → __ats_tmp__obl_s0114.mprage_ns_shft+orig.BRIK
** THD_rename_dataset_files: old header obl_s0114.mprage_ns_shft+acpc.HEAD doesn’t exist!
** THD_rename_dataset_files: old header obl_s0114.mprage_ns_shft+tlrc.HEAD doesn’t exist!
++ 3dWarp: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
++ Authored by: RW Cox
Center distance of 0.000021 mm
Padding …
++ 3dZeropad: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
++ output dataset: ./__ats_tmp__ref_MNI_avg152T1_40pad+tlrc.BRIK
Resampling …
++ 3dcalc: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__ats_tmp__resamp_step+orig.BRIK
++ 3dcalc: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__ats_tmp__resamp+tlrc.BRIK
Clipping -0.000100 764.000100 …
++ 3dcalc: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./__ats_tmp___rs_pre.obl_s0114.mprage_ns+tlrc.BRIK
++ 3drefit: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp___rs_pre.obl_s0114.mprage_ns+tlrc.HEAD
- Changed dataset view type and filenames.
++ 3drefit processed 1 datasets
++ 3drefit: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp__resamp_NN+tlrc.HEAD - Changed dataset view type and filenames.
++ 3drefit processed 1 datasets
++ 3drefit: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp__resamp_edge_art+tlrc.HEAD - Changed dataset view type and filenames.
++ 3drefit processed 1 datasets
Registration (linear final interpolation) …
++ 3dWarpDrive: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
++ Authored by: RW Cox
++ Initial scale factor set to 0.30/143.00=4.8e+02
RMS[0] = 0.412897 0.138407 ITER = 7/137
0.412897
Warping has converged.
++ 3dcopy: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
++ 3dWarp: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
++ Authored by: RW Cox
Applying brain mask
++ 3dcalc: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__ats_tmp__reg_braintlrcstep+orig.BRIK
++ 3dWarp: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
++ Authored by: RW Cox
++ 3drename: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
++ THD_rename_dataset_files: rename __ats_tmp___pad40_pre.obl_s0114.mprage_ns+orig.HEAD → __ats_tmp___pad40_pre.obl_s0114.mprage_ns.skl+orig.HEAD
++ THD_rename_dataset_files: rename __ats_tmp___pad40_pre.obl_s0114.mprage_ns+orig.BRIK → __ats_tmp___pad40_pre.obl_s0114.mprage_ns.skl+orig.BRIK
++ 3dcalc: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__ats_tmp___pad40_pre.obl_s0114.mprage_ns+orig.BRIK
Unpadding …
++ 3dZeropad: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
++ output dataset: ./__ats_tmp___upad40_pre.obl_s0114.mprage_ns+orig.BRIK
++ 3drefit: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp___upad40_pre.obl_s0114.mprage_ns+orig
*+ WARNING: Changing the space of an ORIG view dataset may cause confusion!
*+ WARNING: NIFTI copies will be interpreted as TLRC view (not TLRC space).
*+ WARNING: Consider changing the view of the dataset to TLRC view also
++ 3drefit processed 1 datasets
Changing view of transformed anatomy
++ 3drefit: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp___upad40_pre.obl_s0114.mprage_ns+orig.HEAD
- Changed dataset view type and filenames.
++ 3drefit processed 1 datasets
Setting parent with 3drefit -wset obl_s0114.mprage_ns+orig __ats_tmp___upad40_pre.obl_s0114.mprage_ns+tlrc
++ 3drefit: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp___upad40_pre.obl_s0114.mprage_ns+tlrc
++ 3drefit processed 1 datasets
++ 3drename: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
++ Warning: ignoring +tlrc on new_prefix.
++ THD_rename_dataset_files: rename __ats_tmp___upad40_pre.obl_s0114.mprage_ns+tlrc.HEAD → obl_s0114.mprage_ns+tlrc.HEAD
++ THD_rename_dataset_files: rename __ats_tmp___upad40_pre.obl_s0114.mprage_ns+tlrc.BRIK → obl_s0114.mprage_ns+tlrc.BRIK
Cleanup …
cat_matvec obl_s0114.mprage_ns+tlrc::WARP_DATA -I
if ( ! -f obl_s0114.mprage_ns+tlrc.HEAD ) then
foreach run ( 01 02 )
3dvolreg -verbose -zpad 1 -base vr_base+orig -1Dfile dfile.r01.1D -prefix rm.epi.volreg.r01 -cubic -1Dmatrix_save mat.r01.vr.aff12.1D pb01.s0114.r01.tshift+orig
++ 3dvolreg: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
++ Authored by: RW Cox
++ Reading in base dataset ./vr_base+orig.BRIK
++ Reading input dataset ./pb01.s0114.r01.tshift+orig.BRIK
++ Edging: x=3 y=4 z=2
++ Creating mask for -maxdisp - Automask has 41761 voxels
- 6269 voxels left in -maxdisp mask after erosion
++ Initializing alignment base
++ Starting final pass on 138 sub-bricks: 0…1…2…3…4…5…6…7…8…9…10…11…12…13…14…15…16…17…18…19…20…21…22…23…24…25…26…27…28…29…30…31…32…33…34…35…36…37…38…39…40…41…42…43…44…45…46…47…48…49…50…51…52…53…54…55…56…57…58…59…60…61…62…63…64…65…66…67…68…69…70…71…72…73…74…75…76…77…78…79…80…81…82…83…84…85…86…87…88…89…90…91…92…93…94…95…96…97…98…99…100…101…102…103…104…105…106…107…108…109…110…111…112…113…114…115…116…117…118…119…120…121…122…123…124…125…126…127…128…129…130…131…132…133…134…135…136…137…
++ CPU time for realignment=7.58 s [=0.0549 s/sub-brick]
++ Min : roll=-0.649 pitch=+0.000 yaw=-0.812 dS=-1.036 dL=-0.443 dP=-0.644
++ Mean: roll=-0.470 pitch=+0.864 yaw=-0.526 dS=-0.420 dL=-0.250 dP=-0.365
++ Max : roll=+0.011 pitch=+1.533 yaw=+0.000 dS=+0.041 dL=+0.006 dP=+0.000
++ Max displacements (mm) for each sub-brick:
0.00(0.00) 0.07(0.07) 0.09(0.08) 0.26(0.22) 1.66(1.42) 0.86(0.81) 0.88(0.13) 1.14(0.28) 1.38(0.26) 1.33(0.10) 1.37(0.10) 1.48(0.12) 1.45(0.11) 1.42(0.06) 1.42(0.09) 1.42(0.07) 1.42(0.07) 1.44(0.07) 1.39(0.06) 1.54(0.15) 1.92(0.41) 2.00(0.09) 2.06(0.06) 2.05(0.06) 2.30(0.26) 2.35(0.13) 2.18(0.18) 2.12(0.10) 2.13(0.58) 1.62(0.76) 1.37(0.52) 1.36(0.08) 2.25(1.13) 2.68(0.50) 2.60(0.30) 2.46(0.28) 2.41(0.06) 2.33(0.17) 2.31(0.14) 2.24(0.28) 2.19(0.05) 2.14(0.07) 2.05(0.15) 1.95(0.14) 1.95(0.18) 2.33(0.39) 2.45(0.17) 2.41(0.16) 2.36(0.11) 2.34(0.06) 2.33(0.05) 2.24(0.12) 2.22(0.07) 2.18(0.08) 2.14(0.06) 2.10(0.12) 2.13(0.03) 2.38(0.38) 2.59(1.39) 2.88(0.30) 2.87(0.39) 2.75(0.26) 2.65(0.11) 2.69(0.05) 2.70(0.08) 2.67(0.04) 2.57(0.10) 2.44(0.16) 2.19(0.26) 2.78(0.68) 2.34(0.50) 2.56(0.27) 3.37(0.86) 3.20(0.21) 2.88(0.35) 2.66(0.24) 2.65(0.06) 2.72(0.15) 2.67(0.09) 2.57(0.13) 2.51(0.13) 2.45(0.08) 2.43(0.24) 2.43(0.10) 2.47(0.12) 2.54(0.15) 2.62(0.08) 2.60(0.09) 2.59(0.04) 2.65(0.06) 2.60(0.12) 2.57(0.05) 2.54(0.05) 2.54(0.07) 2.60(0.11) 2.57(0.10) 2.51(0.07) 2.62(0.37) 3.58(1.10) 3.15(0.55) 3.11(0.39) 3.13(0.40) 2.90(0.31) 2.80(0.21) 2.77(0.13) 2.76(0.14) 2.53(0.31) 3.42(0.98) 2.64(0.78) 2.27(0.37) 2.26(0.07) 2.29(0.09) 2.22(0.19) 2.32(0.10) 2.39(0.08) 2.40(0.09) 2.46(0.12) 2.48(0.07) 2.41(0.08) 2.36(0.06) 2.27(0.17) 2.25(0.07) 2.24(0.04) 2.31(0.11) 2.36(0.07) 2.47(0.16) 2.52(0.10) 2.51(0.04) 2.54(0.09) 2.52(0.07) 2.45(0.10) 2.44(0.05) 2.40(0.08) 2.28(0.12) 2.27(0.12) 2.27(0.11) 2.23(0.06) 2.19(0.08)
++ Max displacement in automask = 3.58 (mm) at sub-brick 98
++ Max delta displ in automask = 1.42 (mm) at sub-brick 4
++ Wrote dataset to disk in ./rm.epi.volreg.r01+orig.BRIK
3dcalc -overwrite -a pb01.s0114.r01.tshift+orig -expr 1 -prefix rm.epi.all1
++ 3dcalc: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
++ Authored by: A cast of thousands
*+ WARNING: input ‘a’ is not used in the expression
++ Output dataset ./rm.epi.all1+orig.BRIK
cat_matvec -ONELINE obl_s0114.mprage_ns+tlrc::WARP_DATA -I obl_s0114.mprage_al_junk_mat.aff12.1D -I mat.r01.vr.aff12.1D
** FATAL ERROR: Can’t read file ‘obl_s0114.mprage_al_junk_mat.aff12.1D’
** Program compile date = Oct 24 2016