Hi ptaylor,
Thank you so much for that answer I think now the origin of my problem is now obvious:
3dinfo -space -prefix /home/cgarin/Documents/1_Macaque_MRI/2_Atlas/nmt_1.2/NMT_SS.nii.gz
** AFNI converts NIFTI_datatype=4 (INT16) in file1_Macaque_MRI/2_Atlas/nmt_1.2/NMT_SS.nii.gz to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
ORIG NMT_SS.nii.gz
3dinfo -space -prefix /home/cgarin/Documents/1_Macaque_MRI/3_Nifti5/Oliver2019_02_02/anatT1_warp2std_nsu.nii.gz
ORIG anatT1_warp2std_nsu.nii.gz
But I really don't understand why the space has been modified....
and my code for the co-registration
@animal_warper input anatT1.nii.gz -base 1_Macaque_MRI/2_Atlas/nmt_1.2/NMT_SS.nii.gz -atlas 1_Macaque_MRI/2_Atlas/nmt_1.2/F99_WOcerv_NMT.nii.gz -outdir ouput_dir_a_id
afni_proc.py -subj_id Oliver2019_02_02 /
-script 1_Macaque_MRI/8_Func_AFNI/Oliver2019_02_02/proc.Oliver2019_02_02 /
-scr_overwrite -out_dir 1_Macaque_MRI/8_Func_AFNI/Oliver2019_02_02/Oliver2019_02_02.results /
-blocks tshift align tlrc volreg blur mask scale regress -dsets 1_Macaque_MRI/3_Nifti/Oliver2019_02_02/BOLD_restingstate.nii.gz /
-copy_anat 1_Macaque_MRI/3_Nifti5/Oliver2019_02_02/anatT1_ns.nii.gz -anat_has_skull no -tcat_remove_first_trs 10 /
-volreg_align_to MIN_OUTLIER -volreg_align_e2a -volreg_tlrc_warp -align_opts_aea -cost lpa+zz -giant_move -align_epi_strip_method None /
-tlrc_base 1_Macaque_MRI/2_Atlas/nmt_1.2/NMT_SS.nii.gz', '-tlrc_NL_warp /
-tlrc_NL_warped_dsets 1_Macaque_MRI/3_Nifti5/Oliver2019_02_02/anatT1_warp2std_nsu.nii.gz /
1_Macaque_MRI/3_Nifti5/Oliver2019_02_02/anatT1_shft_al2std_mat.aff12.1D /
1_Macaque_MRI/3_Nifti5/Oliver2019_02_02/anatT1_shft_WARP.nii.gz /
-blur_size 2.0 -regress_censor_motion 0.35 -regress_censor_outliers 0.02 -regress_motion_per_run -regress_est_blur_errts /
-regress_est_blur_epits -regress_run_clustsim no -execute
Let me know if everything sounds good for simple resting state acquisition,
again thanks a lot for the help!
Clément
