Hi Paul,
So, I'm still having issues unfortunately. I'm getting a different error now though.
diary:
++ Starting: @SSwarper v2.33
++ Default OMP_NUM_THREADS is 4
++ Prepare for running @djunct_overlap_check (ver = 0.2)
++ Just copy olay, bc ulay will get regridded
++ My command:
@chauffeur_afni -ulay olapch_0_cp_ulay.nii -pass -pass -olay olapch_1_cp_olay.nii -ulay_range 0% 98% -func_range_perc_nz 98 -cbar Reds_and_Blues -pbar_posonly -set_subbricks 0 0 0 -olay_alpha No -olay_boxed No -opacity 4 -zerocolor black -prefix img00 -montx 1 -monty 1 -montgap 1 -montcolor black -save_ftype JPEG -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean -set_dicom_xyz 0 0 0
\n------------------ start of optionizing ------------------\n
++ Found input file: olapch_0_cp_ulay.nii
++ Found input file: olapch_1_cp_olay.nii
++ Using blowup factor: 2
++ Using opacity: 4
++ Making temporary work directory to copy vis files: ./__tmp_chauf_BBJbFjPHDf2
++ Converted 0 to labels
++ Final subbrick indices: 0 0 0
++ Copy ulay to visualize (volumetric) within user's range:
++ Ulay to be visualized within user range:
[0%, 98%] -> [0.000000, 703.000000]
++ For olay, the 98%ile value leads to
--> upper range value: 1151.000000
++ Dimensions (xyzt): 280 320 208 1
++ (initial) Slice spacing ordered (x,y,z) is: 208 280 320
++ Will have user's chosen: SET_DICOM_XYZ 0 0 0
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :931
[1] 55595
Precompiled binary macos_10.12_local: Dec 7 2020 (Version AFNI_20.3.03 'Vespasian')
+++ Command Echo:
afni -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=4 mont=1x1:208:1:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=4 mont=1x1:280:1:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=4 mont=1x1:320:1:black crop=0:0,0:0 -com SET_PBAR_ALL +99 1 Reds_and_Blues -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 703.000000 -com SET_FUNC_RANGE 1151.000000 -com SET_THRESHNEW 0 * -com SET_FUNC_ALPHA No -com SET_FUNC_BOXED No -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_DICOM_XYZ 0 0 0 -com SAVE_JPEG sagittalimage ./img00.sag blowup=2 -com SAVE_JPEG coronalimage ./img00.cor blowup=2 -com SAVE_JPEG axialimage ./img00.axi blowup=2 -com QUITT ./__tmp_chauf_BBJbFjPHDf2
....\n+* Removing temporary image directory './__tmp_chauf_BBJbFjPHDf2'.\n
[1] Done Xvfb :931 -screen 0 1024x768x24
++ DONE (good exit)
see: ./img00*
+++ Arranging 3 images (each 416x560) into a 3x1 matrix.
You can view image ../init_qc_00_overlap_usrc_obase.jpg with:
aiv ../init_qc_00_overlap_usrc_obase.jpg
\n+* Removing temporary workdir 'o.aw_sub/__workdir_olap_rTdGepEA8Og*'\n
++ DONE! Image output:
o.aw_sub/init_qc_00_overlap_usrc_obase
++ SSW Step 1
++ SSW Step 2
++ SSW Step 3
+++ Command Echo:
3dQwarp -lite -base /Users/whistu/abin/MNI152_2009_template_SSW.nii.gz[1] -lpa -warpscale 1 -source o.aw_sub/anatUAC.sub.nii -weight /Users/whistu/abin/MNI152_2009_template_SSW.nii.gz[2] -allineate -noneg -maxlev 5 -iwarp -awarp -wtgaus 4.5 -inedge -workhard:3:5 -nopenalty -prefix o.aw_sub/junk.SSwarper_NBf0JTU53y0_TAL5.nii -allopt -twobest 11 -twopass -maxrot 45 -maxshf 40 -source_automask+2 -cmass
# mat44 3dAllineate matrix:
0.882100 -0.005909 0.007026 12.393200
0.002741 0.966010 0.191951 -41.969299
-0.018638 -0.055064 0.838204 -27.198299
++ SSW Step 4
** ERROR: program failed in Step 4
*********------ CRASH LOG ------------------------------***********
Fatal Signal 11 (SIGSEGV) received
.......... recent internal history .........................................
+++++++mri_free [7]: {ENTRY (file=mri_free.c line=49) from IW3D_cleanup_improvement {2335 ms}
-------mri_free [7]: EXIT} (file=mri_free.c line=50) to IW3D_cleanup_improvement {2335 ms}
+++++++mri_free [7]: {ENTRY (file=mri_free.c line=49) from IW3D_cleanup_improvement {2335 ms}
-------mri_free [7]: EXIT} (file=mri_free.c line=50) to IW3D_cleanup_improvement {2335 ms}
+++++++IW3D_destroy [7]: {ENTRY (file=mri_nwarp.c line=960) from IW3D_cleanup_improvement {2335 ms}
-------IW3D_destroy [7]: EXIT} (file=mri_nwarp.c line=967) to IW3D_cleanup_improvement {2335 ms}
+++++++IW3D_destroy [7]: {ENTRY (file=mri_nwarp.c line=960) from IW3D_cleanup_improvement {2335 ms}
-------IW3D_destroy [7]: EXIT} (file=mri_nwarp.c line=967) to IW3D_cleanup_improvement {2335 ms}
+++++++IW3D_destroy [7]: {ENTRY (file=mri_nwarp.c line=960) from IW3D_cleanup_improvement {2335 ms}
-------IW3D_destroy [7]: EXIT} (file=mri_nwarp.c line=967) to IW3D_cleanup_improvement {2335 ms}
+++++++INCOR_destroy [7]: {ENTRY (file=thd_incorrelate.c line=1865) from IW3D_cleanup_improvement {2335 ms}
-------INCOR_destroy [7]: EXIT} (file=thd_incorrelate.c line=1867) to IW3D_cleanup_improvement {2335 ms}
------IW3D_cleanup_improvement [6]: EXIT} (file=mri_nwarp.c line=10245) to IW3D_setup_for_improvement {2335 ms}
++++++mri_to_float [6]: {ENTRY (file=mri_to_float.c line=19) from IW3D_setup_for_improvement {2335 ms}
+++++++mri_new_7D_generic [7]: {ENTRY (file=mri_new.c line=48) from mri_to_float {2335 ms}
-------mri_new_7D_generic [7]: EXIT} (file=mri_new.c line=143) to mri_to_float {2339 ms}
+++++++mri_add_name [7]: {ENTRY (file=mri_add_name.c line=19) from mri_to_float {2345 ms}
-------mri_add_name [7]: EXIT} (file=mri_add_name.c line=24) to mri_to_float {2345 ms}
------mri_to_float [6]: EXIT} (file=mri_to_float.c line=94) to IW3D_setup_for_improvement {2358 ms}
++++++mri_to_float [6]: {ENTRY (file=mri_to_float.c line=19) from IW3D_setup_for_improvement {2358 ms}
+++++++mri_new_7D_generic [7]: {ENTRY (file=mri_new.c line=48) from mri_to_float {2358 ms}
-------mri_new_7D_generic [7]: EXIT} (file=mri_new.c line=143) to mri_to_float {2361 ms}
+++++++mri_add_name [7]: {ENTRY (file=mri_add_name.c line=19) from mri_to_float {2370 ms}
-------mri_add_name [7]: EXIT} (file=mri_add_name.c line=24) to mri_to_float {2370 ms}
------mri_to_float [6]: EXIT} (file=mri_to_float.c line=94) to IW3D_setup_for_improvement {2383 ms}
++++++mri_interior_edgeize [6]: {ENTRY (file=mri_intedge.c line=19) from IW3D_setup_for_improvement {2383 ms}
+++++++mri_maxabs [7]: {ENTRY (file=mri_max.c line=98) from mri_interior_edgeize {2383 ms}
-------mri_maxabs [7]: EXIT} (file=mri_max.c line=129) to mri_interior_edgeize {2396 ms}
+++++++mri_new_7D_generic [7]: {ENTRY (file=mri_new.c line=48) from mri_interior_edgeize {2396 ms}
-------mri_new_7D_generic [7]: EXIT} (file=mri_new.c line=143) to mri_interior_edgeize {2400 ms}
mri_interior_edgeize -- call Extract_Gradient_Maxima_3D {2400 ms}
............................................................................
Last STATUS: call Extract_Gradient_Maxima_3D
mri_interior_edgeize
IW3D_setup_for_improvement
IW3D_warpomatic
IW3D_warp_s2bim
3dQwarp
** AFNI compile date = Dec 7 2020
** [[Precompiled binary macos_10.12_local: Dec 7 2020]]
** Program Crash **
