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alfa_dwi_pipeline_io_aug2016.json
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alfa_dwi_pipeline_io_aug2016.json
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{
"dtifit": [
"@ALFA Denoised Corrected DWI Image",
"ALFA DWI FSL DTIFIT Template Filename",
"@ALFA DWI B0 FSL Brain Mask",
"@Motion-corrected Bvec File",
"@Raw Bval File"
],
"eddycorrect": [
"@ALFA Denoised LPCA DWI Image",
">ALFA Denoised Corrected DWI Image"
],
"extractb0": [
"@ALFA Denoised Corrected DWI Image",
">ALFA DWI B0 Map"
],
"ants_t1_to_dwi": [
"@ALFA DWI B0 Brain FSL FAST White matter",
"@ALFA Denoised Nobias SPM Dilated White matter",
"ALFA ANTS Elast T1 to DWI Transformation Template Filename"
],
"ants_mni_to_t1": [
"@ALFA Denoised Nobias T1 Image",
"#/home/grg/data/templates/MNI_atlas_templates/MNI_T1.nii",
"ALFA ANTS SyN MNI to T1 Transformation Template Filename"
],
"ants_dwi_to_t1": [
"@ALFA Denoised Nobias SPM Dilated White matter",
"@ALFA DWI B0 Brain FSL FAST White matter",
"ALFA ANTS Elast DWI to T1 Transformation Template Filename"
],
"warp_t1_to_dwi": [
"@ALFA Denoised Nobias T1 Image",
">ALFA T1 Image Warped to DWI space",
"@ALFA DWI B0 Map",
"@ALFA ANTS Elast T1 to DWI Transformation",
"@ALFA ANTS Elast T1 to DWI Affine Transformation"
],
"warp_aal_to_dwi": [
"@ALFA AAL Atlas Warped to T1 space",
">ALFA AAL Atlas Warped to DWI space",
"@ALFA DWI B0 Map",
"@ALFA ANTS Elast T1 to DWI Transformation",
"@ALFA ANTS Elast T1 to DWI Affine Transformation"
],
"warp_aal_to_t1": [
"#/home/grg/data/templates/MNI_atlas_templates/aal_MNI_V4.nii",
">ALFA AAL Atlas Warped to T1 space",
"@ALFA Denoised Nobias T1 Image",
"@ALFA ANTS SyN MNI to T1 Transformation",
"@ALFA ANTS SyN MNI to T1 Affine Transformation"
],
"warp_md_to_mni": [
"@ALFA DWI MD Map Warped to T1 space",
">ALFA DWI MD Map Warped to MNI space",
"#/home/grg/data/templates/MNI_atlas_templates/MNI_T1.nii",
"@ALFA ANTS SyN MNI to T1 Affine Transformation",
"@ALFA ANTS SyN MNI to T1 Inverse Transformation"
],
"warp_md_to_t1": [
"@ALFA Mean Diffusivity Image",
">ALFA DWI MD Map Warped to T1 space",
"@ALFA Denoised Nobias T1 Image",
"@ALFA ANTS Elast DWI to T1 Transformation",
"@ALFA ANTS Elast DWI to T1 Affine Transformation"
],
"warp_fa_to_t1": [
"@ALFA Fractional Anisotropy Image",
">ALFA DWI FA Map Warped to T1 space",
"@ALFA Denoised Nobias T1 Image",
"@ALFA ANTS Elast DWI to T1 Transformation",
"@ALFA ANTS Elast DWI to T1 Affine Transformation"
],
"warp_fa_to_mni": [
"@ALFA DWI FA Map Warped to T1 space",
">ALFA DWI FA Map Warped to MNI space",
"#/home/grg/data/templates/MNI_atlas_templates/MNI_T1.nii",
"@ALFA ANTS SyN MNI to T1 Affine Transformation",
"@ALFA ANTS SyN MNI to T1 Inverse Transformation"
],
"warp_l1_to_t1": [
"@ALFA L1 Image",
">ALFA DWI L1 Map Warped to T1 space",
"@ALFA Denoised Nobias T1 Image",
"@ALFA ANTS Elast DWI to T1 Transformation",
"@ALFA ANTS Elast DWI to T1 Affine Transformation"
],
"warp_l1_to_mni": [
"@ALFA DWI L1 Map Warped to T1 space",
">ALFA DWI L1 Map Warped to MNI space",
"#/home/grg/data/templates/MNI_atlas_templates/MNI_T1.nii",
"@ALFA ANTS SyN MNI to T1 Affine Transformation",
"@ALFA ANTS SyN MNI to T1 Inverse Transformation"
],
"warp_rd_to_t1": [
"@ALFA Radial Diffusivity Image",
">ALFA DWI RD Map Warped to T1 space",
"@ALFA Denoised Nobias T1 Image",
"@ALFA ANTS Elast DWI to T1 Transformation",
"@ALFA ANTS Elast DWI to T1 Affine Transformation"
],
"warp_rd_to_mni": [
"@ALFA DWI RD Map Warped to T1 space",
">ALFA DWI RD Map Warped to MNI space",
"#/home/grg/data/templates/MNI_atlas_templates/MNI_T1.nii",
"@ALFA ANTS SyN MNI to T1 Affine Transformation",
"@ALFA ANTS SyN MNI to T1 Inverse Transformation"
],
"fslfast": [
"!ALFA DWI B0 FSL Masked Brain",
">ALFA DWI B0 FSL Masked Brain"
],
"rotcorr": [
"@Raw Bvec File",
">Motion-corrected Bvec File",
"@FSL Eddy current Correction Logfile"
],
"denoising": [
"@ALFA DWI Raw Image"
],
"denoise_t1": [
"@ALFA T1 Raw Image"
],
"fslbet.25": [
"@ALFA DWI B0 Map",
">ALFA DWI B0 FSL Masked Brain"
],
"roistats_md": [
"@ALFA AAL Atlas Warped to DWI space",
"@ALFA Mean Diffusivity Image",
">ALFA Mean Diffusivity (AAL) ROI stats in T1 space"
],
"roistats_md_mni": [
"#/home/grg/data/templates/MNI_atlas_templates/aal_MNI_V4.nii",
"@ALFA DWI MD Map Warped to MNI space",
">ALFA Mean Diffusivity (AAL) ROI stats in MNI space"
],
"roistats_fa": [
"@ALFA AAL Atlas Warped to DWI space",
"@ALFA Fractional Anisotropy Image",
">ALFA Fractional Anisotropy (AAL) ROI stats in T1 space"
],
"roistats_fa_mni": [
"#/home/grg/data/templates/MNI_atlas_templates/aal_MNI_V4.nii",
"@ALFA DWI FA Map Warped to MNI space",
">ALFA Fractional Anisotropy (AAL) ROI stats in MNI space"
],
"roistats_l1": [
"@ALFA AAL Atlas Warped to DWI space",
"@ALFA L1 Image",
">ALFA Axial Diffusivity (AAL) ROI stats in T1 space"
],
"roistats_l1_mni": [
"#/home/grg/data/templates/MNI_atlas_templates/aal_MNI_V4.nii",
"@ALFA DWI L1 Map Warped to MNI space",
">ALFA Axial Diffusivity (AAL) ROI stats in MNI space"
],
"roistats_rd": [
"@ALFA AAL Atlas Warped to DWI space",
"@ALFA Radial Diffusivity Image",
">ALFA Radial Diffusivity (AAL) ROI stats in T1 space"
],
"roistats_rd_mni": [
"#/home/grg/data/templates/MNI_atlas_templates/aal_MNI_V4.nii",
"@ALFA DWI RD Map Warped to MNI space",
">ALFA Radial Diffusivity (AAL) ROI stats in MNI space"
],
"dilate":[
"@ALFA Denoised Nobias SPM White matter",
">ALFA Denoised Nobias SPM Dilated White matter"
],
"radial":[
"@ALFA L2 Image",
"@ALFA L3 Image",
">ALFA Radial Diffusivity Image"
],
"smooth_md":[
"@ALFA DWI MD Map Warped to MNI space",
">ALFA DWI MD Smoothed Map Warped to MNI space"
],
"smooth_fa":[
"@ALFA DWI FA Map Warped to MNI space",
">ALFA DWI FA Smoothed Map Warped to MNI space"
],
"smooth_l1":[
"@ALFA DWI L1 Map Warped to MNI space",
">ALFA DWI L1 Smoothed Map Warped to MNI space"
],
"smooth_rd":[
"@ALFA DWI RD Map Warped to MNI space",
">ALFA DWI RD Smoothed Map Warped to MNI space"
],
"spm12":["@ALFA Denoised Nobias T1 Image"
],
"nipype_spm12":["@ALFA Denoised Nobias T1 Image"
]
}