anat image cannot be matched to standard space

AFNI Message Board
1

When I do the preprocessing of a child (3 years old), the program always makes mistakes in registering to the standard space.I found the template on the Internet, not AFNI’s.
problem: 3dNwarpApply -nwarp “./anat.un.aff.qw_WARP.nii anat.un.aff.Xat.1D” -master ./base.nii -source /media/hjr/zlw/SCNU_ASD/test/1110083/1110083.results/T1+orig -prefix ./T1.aw.nii
++ 3dNwarpApply: AFNI version=AFNI_20.2.06 (Jul 23 2020) [64-bit]
++ Authored by: Zhark the Warped
++ -master dataset is ‘./base.nii’
++ opened source dataset ‘/media/hjr/zlw/SCNU_ASD/test/1110083/1110083.results/T1+orig’
++ Processing -nwarp
Fatal Signal 11 (SIGSEGV) received
THD_nwarp_regrid
IW3D_set_geometry_nwarp_catlist
IW3D_read_nwarp_catlist
3dNwarpApply
Bottom of Debug Stack
** Command line was:
3dNwarpApply -nwarp ‘./anat.un.aff.qw_WARP.nii anat.un.aff.Xat.1D’ -master ./base.nii -source /media/hjr/zlw/SCNU_ASD/test/1110083/1110083.results/T1+orig -prefix ./T1.aw.nii
** AFNI version = AFNI_20.2.06 Compile date = Jul 23 2020
** [[Precompiled binary linux_ubuntu_16_64: Jul 23 2020]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
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** Crash log is appended to file /home/hjr/.afni.crashlog
AFNI filename:
initial : ./T1.aw.nii
prefix : T1.aw
view :
exten. : .nii
type : NIFTI
On Disk : 0
Row Sel :
Col Sel :
Node Sel:
RangeSel:
#**ERROR Failed in warping step
** ERROR - script failed
3dbucket: No match.

my she’ll: afni_proc.py -subj_id $subj_id
-dsets $subj_indir/rest.nii.gz
-copy_anat $subj_indir/T1.nii
-anat_has_skull no
-blocks despike tshift align tlrc volreg blur mask regress
-tcat_remove_first_trs 3
-align_opts_aea -cost lpc+ZZ
-tlrc_base /media/hjr/zlw/SCNU_ASD/template/infant2yrwithCerebellum.nii
-tlrc_NL_warp
-volreg_align_to MIN_OUTLIER
-volreg_align_e2a
-volreg_tlrc_warp
-volreg_warp_dxyz 3
-blur_size 6.0
-mask_epi_anat yes
-mask_segment_anat yes
-mask_segment_erode yes
-regress_censor_motion 0.3
-regress_censor_outliers 0.1
-regress_bandpass 0.01 0.1
-regress_ROI WMe CSFe
-regress_apply_mot_types demean deriv
-regress_est_blur_epits
-regress_est_blur_errts
Finally, I would like to say that only a few subjects will have such a situation, and the vast majority of other subjects can use this script to complete the preprocessing

2

Sometimes, the header of the original anatomical has problems that produce bad coordinates or orientations. These problems can make the application of warps fail. One solution is to move the original datasets over the center of the template. It’s also possible the template you downloaded has problems that can be too far away from the original data. You might be able to get an idea of this by doing 3dinfo on each of them. If the template looks like it’s roughly centered over (0,0,0), then you can run @Align_Centers with that template as the base. That will remove the large translation in the transformation.

Also, you may be interested that we have worked with a couple other groups to develop both a 2-year-old template and a 4-year-old template. Let me know if that’s of interest, and we can discuss. We also provide on our site the UNC 2-year-old template as part of their infant package.

https://afni.nimh.nih.gov/pub/dist/atlases/UNC_Infant_Atlases/V1.0/