Hi,
I try to run the following command to coregistrate macaque fMRI images to their anatomical but i get an error that i absolutely don't understand. If someone has an idea of what it's going on it could be extremely useful !
tks !!
Standard error:
++ OpenMP thread count = 15
++ 3dQwarp: AFNI version=Debian-16.2.07~dfsg.1-5~nd14.04+1 (Jun 12 2017) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
++ Starting 3dAllineate (affine register) command:
3dAllineate -base /home/Promane/2014-ROMANE/5_Experimental-Plan-Experiments-Results/macaque/Clement/analysis/Newcastle/ses-0022/sub-032097/sub-032097_ses-002_run-1_T1w_unifized_shr_in_func_space_warpSl0_resample.nii.gz -source /home/Promane/2014-ROMANE/5_Experimental-Plan-Experiments-Results/macaque/Clement/analysis/Newcastle/ses-0022/sub-032097/sub-032097_ses-002_task-resting_run-2_bold_tshiftAv_tstat_correctedSl0_resample.nii.gz -prefix XYZ_2_50dSl8qi8HyAoKOU4B2g.nii -1Dmatrix_save XYZ_2_50dSl8qi8HyAoKOU4B2g -cmass -final wsinc5 -float -master BASE -twobest 7 -parfix 1 0 -parfix 2 0 -parfix 3 0 -parfix 4 0 -parfix 5 0 -parfix 6 0 -parfix 7 0 -parfix 9 0 -parfix 10 0 -parfix 12 0 -zclip -fineblur 4.44
++ ###########################################################
++ 3dAllineate: AFNI version=Debian-16.2.07~dfsg.1-5~nd14.04+1 (Jun 12 2017) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: /home/Promane/2014-ROMANE/5_Experimental-Plan-Experiments-Results/macaque/Clement/analysis/Newcastle/ses-0022/sub-032097/sub-032097_ses-002_task-resting_run-2_bold_tshiftAv_tstat_correctedSl0_resample.nii.gz
++ Base dataset: /home/Promane/2014-ROMANE/5_Experimental-Plan-Experiments-Results/macaque/Clement/analysis/Newcastle/ses-0022/sub-032097/sub-032097_ses-002_run-1_T1w_unifized_shr_in_func_space_warpSl0_resample.nii.gz
++ Loading datasets
++ 1144900 voxels in source_automask+0
++ Zero-pad: xbot=4 xtop=0
++ Zero-pad: ybot=4 ytop=4
+ 2D image registration: orientation is axial
++ Computing -autobox
++ 483399 voxels [41.8%] in weight mask
++ Number of points for matching = 227197
++ base dataset is 2D ==> froze out-of-plane affine parameters
+ Altering fixed param#3 [z-shift]
+ Altering fixed param#5 [x-angle]
+ Altering fixed param#6 [y-angle]
+ Altering fixed param#9 [z-scale]
+ Altering fixed param#12 [z/y-shear]
*+ WARNING: Disabling twopass because no free parameters in first 6!?
++ OpenMP thread count = 15
++ ======= Allineation of 1 sub-bricks using Hellinger metric =======
++ ========== sub-brick #0 ========== [total CPU to here=0.0 s]
++ *** Fine pass begins ***
+ Final fine fit Parameters:
x-shift= 0.0000 y-shift= 0.0000 z-shift= 0.0000
z-angle= 0.0000 x-angle= 0.0000 y-angle= 0.0000
x-scale= 0.0000 y-scale= 1.0150 z-scale= 0.0000
y/x-shear= 0.0000 z/x-shear= 0.0000 z/y-shear= 0.0000
++ Output dataset ./XYZ_2_50dSl8qi8HyAoKOU4B2g.nii
++ Wrote -1Dmatrix_save XYZ_2_50dSl8qi8HyAoKOU4B2g.aff12.1D
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 1.3
++ ###########################################################
++ ### Please check results visually for alignment quality ###
++ ###########################################################
++ 3dQwarp: replacing source dataset with 3dAllineate result /home/Promane/2014-ROMANE/5_Experimental-Plan-Experiments-Results/macaque/Clement/analysis/Newcastle/ses-0022/sub-032097/sub-032097_ses-002_task-resting_run-2_bold_tshiftAv_tstat_correctedSl0_resample_qw_Allin.nii
+ 3dAllineate output files have been renamed
++ Dataset zero-pad: xbot=119 xtop=0 ybot=119 ytop=119 zbot=0 ztop=0 voxels
++ Weightizing the base image
++ +++++++++++ Begin warp optimization: base=/home/Promane/2014-ROMANE/5_Experimental-Plan-Experiments-Results/macaque/Clement/analysis/Newcastle/ses-0022/sub-032097/sub-032097_ses-002_run-1_T1w_unifized_shr_in_func_space_warpSl0_resample.nii.gz source=/home/Promane/2014-ROMANE/5_Experimental-Plan-Experiments-Results/macaque/Clement/analysis/Newcastle/ses-0022/sub-032097/sub-032097_ses-002_task-resting_run-2_bold_tshiftAv_tstat_correctedSl0_resample_qw_Allin.nii
++ AFNI warpomatic: 1189 x 1308 x 1 volume ; autobbox = 112..912 113..1195 0..0 [clock= 1s 821ms]
lev=0 12..1012 0..1307 0..0: [first cost=0.96541] .. done [cost:0.96541==>0.96209]
lev=1 patch=893x981x1 [clock= 13s 230ms].... done [cost:0.96209==>0.95949 ; 4 patches optimized, 0 skipped]
lev=2 patch=669x737x1 [clock= 23s 278ms]..... done [cost:0.95949==>0.95896 ; 5 patches optimized, 1 skipped]
lev=3 patch=503x553x1 [clock= 28s 101ms]..... done [cost:0.95896==>0.95730 ; 10 patches optimized, 2 skipped]
lev=4 patch=377x415x1 [clock= 35s 700ms].... done [cost:0.95730==>0.95614 ; 16 patches optimized, 4 skipped]
lev=5 patch=283x311x1 [clock= 43s 607ms]. done [cost:0.95614==>0.95542 ; 30 patches optimized, 12 skipped]
lev=6 patch=211x233x1 [clock= 52s 215ms].... done [cost:0.95542==>0.95441 ; 50 patches optimized, 22 skipped]
lev=7 patch=159x175x1 [clock= 1m 5s 271ms] done [cost:0.95441==>0.95378 ; 83 patches optimized, 37 skipped]
lev=8 patch=119x131x1 [clock= 1m 20s 579ms]... done [cost:0.95378==>0.95316 ; 152 patches optimized, 86 skipped]
lev=9 patch=89x99x1 [clock= 1m 42s 552ms]... done [cost:0.95316==>0.95247 ; 255 patches optimized, 141 skipped]
lev=10 patch=67x73x1 [clock= 2m 14s 854ms].... done [cost:0.95247==>0.95157 ; 451 patches optimized, 269 skipped]
lev=11 patch=51x55x1 [clock= 3m 6s 297ms]...... done [cost:0.95157==>0.95065 ; 788 patches optimized, 492 skipped]
lev=12 patch=37x41x1 [clock= 4m 31s 360ms]............ done [cost:0.95065==>0.94968 ; 1460 patches optimized, 970 skipped]
lev=13 patch=25x25x1 [clock= 7m 4s 751ms]................. done [cost:0.94968==>0.94835 ; 3616 patches optimized, 2414 skipped]
++ ========== total number of parameters 'optimized' = 110790
++ Output dataset /home/Promane/2014-ROMANE/5_Experimental-Plan-Experiments-Results/macaque/Clement/analysis/Newcastle/ses-0022/sub-032097/sub-032097_ses-002_task-resting_run-2_bold_tshiftAv_tstat_correctedSl0_resample_qw.nii.gz
++ Output dataset /home/Promane/2014-ROMANE/5_Experimental-Plan-Experiments-Results/macaque/Clement/analysis/Newcastle/ses-0022/sub-032097/sub-032097_ses-002_task-resting_run-2_bold_tshiftAv_tstat_correctedSl0_resample_qw_WARP.nii.gz
++ Inverting warp *
Fatal Signal 11 (SIGSEGV) received
Return code: 1
