I am trying to run 3dQwarp on denoised T1 images. The images were originally in .mnc format and I converted them to NIFTI using 3dcalc (-expr ‘a’ -prefix ‘name.nii’) and then ran them through an MRI denoising package in Matlab. When I use 3dQwarp to warp the to the MNI space, it fails. Crash log is below. Any idea what is going on?
------ CRASH LOG ------------------------------**
Fatal Signal 11 (SIGSEGV) received
… recent internal history …
----------mri_new_7D_generic [10]: EXIT} (file=mri_new.c line=142) to mri_to_float
++++++++++mri_add_name [10]: {ENTRY (file=mri_add_name.c line=19) from mri_to_float
----------mri_add_name [10]: EXIT} (file=mri_add_name.c line=24) to mri_to_float
---------mri_to_float [9]: EXIT} (file=mri_to_float.c line=94) to mri_quantile
+++++++++mri_free [9]: {ENTRY (file=mri_free.c line=49) from mri_quantile
mri_free – call killpurge
++++++++++mri_killpurge [10]: {ENTRY (file=mri_purger.c line=259) from mri_free
mri_killpurge – check if im==NULL ptr=0x240e4d8 OK
mri_killpurge – can’t killpurge NULL fname!
----------mri_killpurge [10]: EXIT} (file=mri_purger.c line=270) to mri_free
mri_free – free ptr
mri_free – free im
---------mri_free [9]: EXIT} (file=mri_free.c line=67) to mri_quantile
--------mri_quantile [8]: EXIT} (file=mri_percents.c line=778) to INCOR_clipate
++++++++mri_free [8]: {ENTRY (file=mri_free.c line=49) from INCOR_clipate
mri_free – call killpurge
+++++++++mri_killpurge [9]: {ENTRY (file=mri_purger.c line=259) from mri_free
mri_killpurge – check if im==NULL ptr=0x23e2478 OK
mri_killpurge – can’t killpurge NULL fname!
---------mri_killpurge [9]: EXIT} (file=mri_purger.c line=270) to mri_free
mri_free – free ptr
mri_free – free im
--------mri_free [8]: EXIT} (file=mri_free.c line=67) to INCOR_clipate
-------INCOR_clipate [7]: EXIT} (file=thd_incorrelate.c line=684) to INCOR_2Dhist_xyclip
------INCOR_2Dhist_xyclip [6]: EXIT} (file=thd_incorrelate.c line=703) to IW3D_setup_for_improvement
++++++IW3D_create [6]: {ENTRY (file=mri_nwarp.c line=814) from IW3D_setup_for_improvement
------IW3D_create [6]: EXIT} (file=mri_nwarp.c line=836) to IW3D_setup_for_improvement
++++++IW3D_load_energy [6]: {ENTRY (file=mri_nwarp.c line=1923) from IW3D_setup_for_improvement
IW3D_load_energy – get/create je/se arrays
IW3D_load_energy – set dhhar → 0
IW3D_load_energy – start the work (=energy; get it?)
…
** Command line was:
3dQwarp -allineate -base /net/mci/IMAGENE/NIFTI_CENTRAL/MaskedBrainsTest/cerebellum_atlas/MNI152_1mm_uni+tlrc -source /net/mci/IMAGENE/NIFTI_CENTRAL/MaskedBrainsTest/forDiana/E004_V1/E004_V1_denoised_strip.nii -prefix /net/mci/IMAGENE/NIFTI_CENTRAL/MaskedBrainsTest/forDiana/E004_V1/E004_V1_denoised_strip_warp.nii
…
Last STATUS: start the work (=energy; get it?)
IW3D_load_energy
IW3D_setup_for_improvement
IW3D_warpomatic
IW3D_warp_s2bim
3dQwarp
** Command line was:
3dQwarp -allineate -base /net/mci/IMAGENE/NIFTI_CENTRAL/MaskedBrainsTest/cerebellum_atlas/MNI152_1mm_uni+tlrc -source /net/mci/IMAGENE/NIFTI_CENTRAL/MaskedBrainsTest/forDiana/E004_V1/E004_V1_denoised_strip.nii -prefix /net/mci/IMAGENE/NIFTI_CENTRAL/MaskedBrainsTest/forDiana/E004_V1/E004_V1_denoised_strip_warp.nii
** AFNI compile date = Oct 9 2016
** [[Precompiled binary linux_xorg7_64: Oct 9 2016]]
** Program Crash **