Table of Contents

AFNI analysis

Converting individual (ACPC) monkey brains to NMT

3dAllineate -1Dmatrix_apply curius_anat_composite_linear_to_template.1D -prefix CU_NMT -source CUclean_20130627_ACPC.nii 
3dNwarpApply -nwarp curius_anat_shft_WARP.nii.gz -source CU_NMT+tlrc.BRIK
3dAFNItoNIFTI CU_NMT_Nwarp+tlrc.BRIK
 
3dAllineate -1Dmatrix_apply bacchus_2_anat_composite_linear_to_template.1D -prefix BA_NMT -source BA_noclean_20140711_ACPC_brain_NE_0.5.nii
3dNwarpApply -nwarp bacchus_2_anat_shft_WARP.nii.gz -source BA_NMT+tlrc.BRIK
3dAFNItoNIFTI BA_NMT_Nwarp+tlrc.BRIK

Converting VMPs from original ACPC space to NMT

E.g. Y:\MRI\Curius\2NMT\vmp

Original vmp: dPul_p.vmp, “nominal” res 2 mm, actual 1 mm

The approach works with multiple maps within vmp 

vmp.ExportNifti('dPul_p.nii'); % or NE GUI
ne_change_nii_header_resolution('dPul_p.nii',1);
igor@alex-Precision-T3610:~/VMP_warps$
cp /mnt/KognitiveNeurowissenschaften/DAG/MRI/Curius/2NMT/vmp/dPul_p.nii .
3dAllineate -master CU_NMT_Nwarp.nii -newgrid 1 -1Dmatrix_apply curius_anat_composite_linear_to_template.1D -prefix dPul_p -source  dPul_p.nii
3dNwarpApply -nwarp curius_anat_shft_WARP.nii.gz -source dPul_p+tlrc.BRIK
3dAFNItoNIFTI dPul_p_Nwarp+tlrc.BRIK
sudo cp dPul_p_Nwarp.nii  /mnt/KognitiveNeurowissenschaften/DAG/MRI/Curius/2NMT/vmp/
ne_change_nii_header_resolution('dPul_p_Nwarp.nii',2);
ne_afni_nii2vmp('dPul_p_Nwarp.nii','t',2,'','dPul_p.vmp');

Converting electrode localization prob. maps VMPs from original ACPC space to NMT

E.g. Y:\MRI\Curius\2NMT\electrode_localization

Original vmp: el_dPul_p.vmp, “nominal” res 1 mm, actual 0.5 mm 

ne_vmp2vmr2nifti('el_dPul_p.vmp','CUclean_20130627_ACPC_1mm.vmr');
ne_change_nii_header_resolution('el_dPul_p.nii',0.5);
igor@alex-Precision-T3610:~/VMP_warps$
cp /mnt/KognitiveNeurowissenschaften/DAG/MRI/Curius/2NMT/electrode_localization/el_dPul_p.nii .
3dAllineate -master CU_NMT_Nwarp.nii -1Dmatrix_apply curius_anat_composite_linear_to_template.1D -prefix el_dPul_p -source  el_dPul_p.nii
3dNwarpApply -nwarp curius_anat_shft_WARP.nii.gz -source el_dPul_p+tlrc.BRIK
3dAFNItoNIFTI el_dPul_p_Nwarp+tlrc.BRIK
sudo cp el_dPul_p_Nwarp.nii  /mnt/KognitiveNeurowissenschaften/DAG/MRI/Curius/2NMT/electrode_localization/
ne_change_nii_header_resolution('el_dPul_p_Nwarp.nii',1);
ne_afni_nii2vmp('el_dPul_p_Nwarp.nii','t',1);