afni.nimh.nih.gov

Hi-

I split this question to a new thread from here:
[afni.nimh.nih.gov]
because it is a somewhat separate question, and the thread has wandered further afield.

--pt

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Hi,
I have exactly the same problem as you for NMT to the anat space.
This command has also worked for other animals.

'3dNwarpApply', '-overwrite', '-ainterp', 'NN', '-nwarp', '/lastV/anatT1_unifized_affine_general_warped_WARP.nii.gz', '/lastV/anatT1_unifized_masked_aff.aff12.1D', '-iwarp', '-source', '/Atlas_centr.nii.gz', '-master', '/anatT1.nii.gz', '-prefix', '/Atlas_in_anat.nii.gz']'

++ Processing -nwarp 
 +  -- invert max|AA|=296.562225
 +   - init nstep=10 qq=1/2^10=0.000977
 +   - start iterations: normAA=12.668444 inewtfac=0.333000
 +   - iterate 1 nrat=0.015831
 +   - iterate 2 nrat=0.015625
 +   - iterate 3 nrat=0.008611
 +   - iterate 4 nrat=0.005700
 +   - iterate 5 nrat=0.004121
 +   - iterate 6 nrat=0.002091
 +   - iterate 7 nrat=0.001215
 +   - iterate 8 nrat=0.000514
 +   - switching from linear interp
 +   - iterate 9 nrat=0.000185
 +   - iterate 10 nrat=0.000071
 +  -- iteration converged
++ Warping:** ERROR: EDIT_full_copy: can't malloc -2134449508 bytes for new sub-brick 0
 +    Dataset ./InvertedWarp+orig.HEAD

Fatal Signal 11 (SIGSEGV) received
     THD_nwarp_regrid
    IW3D_set_geometry_nwarp_catlist
   IW3D_read_nwarp_catlist
  3dNwarpApply
 Bottom of Debug Stack
** AFNI version = AFNI_19.3.18  Compile date = Dec 27 2019
** [[Precompiled binary linux_ubuntu_16_64: Dec 27 2019]]
** 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.
** You may later be asked to upload data to help debug.
** Crash log is appended to file /home/cgarin/.afni.crashlog

I try to apply the inverse of a transfo based on the anat to NMT that has been inspected visually.
Did you managed to fixe this problem?

"2. I ran two stages transformation. First did the nonlinear warp, saved the result. Then ran the affine. The results looked reasonable. However I have to resample twice in this regime."
Which AFNI program did you use to separately apply the nonlinear warp and the affine (you can't use 3dNwarpApply for the affine?)?

Thanks a lot,
Clément



Edited 1 time(s). Last edit at 01/08/2020 01:29PM by ptaylor.