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analysis:fmri:afni [2021/03/04 15:05] – created igorkagananalysis:fmri:afni [2022/12/29 07:15] (current) – external edit 127.0.0.1
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 ====== AFNI analysis ====== ====== AFNI analysis ======
  
-===== Converting individual monkey brains to NMT =====+===== Converting individual (ACPC) monkey brains to NMT =====
  
-<code>+<code bash>
  
 3dAllineate -1Dmatrix_apply curius_anat_composite_linear_to_template.1D -prefix CU_NMT -source CUclean_20130627_ACPC.nii  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 3dNwarpApply -nwarp curius_anat_shft_WARP.nii.gz -source CU_NMT+tlrc.BRIK
- 
 3dAFNItoNIFTI CU_NMT_Nwarp+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
  
 </code> </code>
 +
 +===== 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
 +
 +<code matlab>
 +vmp.ExportNifti('dPul_p.nii'); % or NE GUI
 +ne_change_nii_header_resolution('dPul_p.nii',1);
 +</code>
 +
 +<code bash>
 +
 +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/
 +
 +</code>
 +
 +<code matlab>
 +ne_change_nii_header_resolution('dPul_p_Nwarp.nii',2);
 +ne_afni_nii2vmp('dPul_p_Nwarp.nii','t',2,'','dPul_p.vmp');
 +</code>
 +
 +===== 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 
 +
 +<code matlab>
 +ne_vmp2vmr2nifti('el_dPul_p.vmp','CUclean_20130627_ACPC_1mm.vmr');
 +ne_change_nii_header_resolution('el_dPul_p.nii',0.5);
 +</code>
 +
 +<code bash>
 +
 +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/
 +
 +</code>
 +
 +<code matlab>
 +ne_change_nii_header_resolution('el_dPul_p_Nwarp.nii',1);
 +ne_afni_nii2vmp('el_dPul_p_Nwarp.nii','t',1);
 +</code>
 +
analysis/fmri/afni.1614870333.txt.gz · Last modified: 2022/12/29 07:15 (external edit)