Hi again, so I ran a couple of different settings. First of all I tested running with just linear warping and that works, even without running the 3dAlignCenters function prior to the analysis script.

Then I tried a couple of different cost functions and non-linear warping by running 5 different afni_proc sricpts with these settings:

1.
-align_opts_aea \
-giant_move \
-cost lpa \

2.
-align_opts_aea \
-giant_move \
-cost lpc+ZZ \

3.
-align_opts_aea \
-giant_move \
-cost lpc+ \

4.
-align_opts_aea \
-giant_move \
-cost mi \

5.
-align_opts_aea \
-giant_move \
-resample off \

All of these still result in the same error:

3dNwarpApply -source TEST_sT1W_3D_TFE_SENSE_4_1_shft+orig -master anat_final.AB123_risk_Regress+tlrc -ainterp wsinc5 -nwarp anat.un.aff.qw_WARP.nii anat.un.aff.Xat.1D TEST_sT1W_3D_TFE_SENSE_4_1_shft_al_keep_mat.aff12.1D -prefix anat_w_skull_warped
++ 3dNwarpApply: AFNI version=AFNI_16.0.05 (Feb 10 2016) [64-bit]
++ Authored by: Zhark the Warped
*** Error in `3dNwarpApply': malloc(): memory corruption: 0x000000000{SOME NUMBER} ***

Fatal Signal 6 (SIGABRT) received
3dNwarpApply
Bottom of Debug Stack
** AFNI version = AFNI_16.0.05 Compile date = Feb 10 2016
** [[Precompiled binary linux_openmp_64: Feb 10 2016]]
** 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.

So now I don't know what to do. You mentioned doing it stepise:

Quote
Daniel Glen
- epi to anat (align_epi_anat.py), anat to template affine (@auto_tlrc), anat to template nonlinear (auto_warp.py/3dQwarp)

I'm not that used to running these functions by themselves, I usually use afni_proc. Are there some specific settings I should try?

Thank you so much!



Edited 1 time(s). Last edit at 07/05/2016 07:17AM by Robin.