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Documentation::DTI-TK:Documentation:Image Mapping Options After Registration
Documentation.OptionspostReg History
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->This warps the '''native''' subject DTI data @@subj1.nii.gz@@ to the space defined by the DTI template @@template.nii.gz@@ using the DTI-TK estimated transformations @@subj1.aff@@ and @@subj1_aff_diffeo.df.nii.gz@@, such that the output voxel spacing is 2x2x2.
to:
->This warps the '''native''' subject DTI data @@subj1.nii.gz@@ to the space defined by the DTI template @@template.nii.gz@@ using the DTI-TK estimated transformations @@subj1.aff@@ and @@subj1_aff_diffeo.df.nii.gz@@, such that the output voxel spacing is 2x2x2. The output from the script includes the normalized DTI data @@subj1_diffeo.nii.gz@@ and the combined transformation (displacement field) @@subj1_combined.df.nii.gz@@.
Changed lines 48-53 from:
->'''A pair of convenient scripts for warping your DTI data to the template space'''
->'''Warping your scalar-valued data'''
->There is a similar command for warping scalar volumes called ''deformationScalarVolume''. The example below shows how to warp the FA map of the same image with this command.
to:
->'''A pair of convenience scripts for warping your DTI data to the template space'''
->Given how often we need to do this, we provide two convenience scripts for this task: @@dti_warp_to_template@@ and @@dti_warp_to_template_group@@. The former combines the computation of the combined warp described above and the warping into a single command. The latter makes this even easier for a collection of subjects.
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deformationScalarVolume -in subj_fa.nii.gz -trans subj_combined.df.nii.gz -target mean_initial.nii.gz -out subj_fa_combined.nii.gz
to:
dti_warp_to_template subj1.nii.gz template.nii.gz 2 2 2 Changed lines 55-64 from:
->Note that you can compute the warped FA map of a subject DTI volume in two ways. One is to warp the DTI volume and then compute the FA map. Or you can first compute the FA map then warp the FA map. Many people in the DTI community argue that the former is preferred because the interpolation accounts for the tensorial properties.
>><<
!!!Combined displacement field from the template space to the native space (:showhide init=hide div=combined_displacement_template_to_native:)
>>id=combined_displacement_template_to_native padding=5px<<
Use the same example as the one above. We will compute the inverse of the affine transformation and that of the deformable transformation, then combine them appropriately. The steps are as follows:
->1. compute the inverse of the affine transformation with the command ''affine3Dtool''
to:
->This warps the '''native''' subject DTI data @@subj1.nii.gz@@ to the space defined by the DTI template @@template.nii.gz@@ using the DTI-TK estimated transformations @@subj1.aff@@ and @@subj1_aff_diffeo.df.nii.gz@@, such that the output voxel spacing is 2x2x2.
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affine3Dtool -in subj.aff -invert -out subj_inv.aff
to:
dti_warp_to_template_group subjs.txt template.nii.gz 2 2 2 Changed lines 60-64 from:
The computed inverse will be stored in subj_inv.aff'.
->2. compute the inverse of the deformable transformation with the command ''dfToInverse''
to:
->This applies the same command as above to a collection of the '''native''' subject DTI data.
->'''Warping your scalar-valued data'''
->There is a similar command for warping scalar volumes called ''deformationScalarVolume''. The example below shows how to warp the FA map of the same image with this command.
Changed line 67 from:
dfToInverse -in subj_aff_diffeo.df.nii.gz
to:
deformationScalarVolume -in subj_fa.nii.gz -trans subj_combined.df.nii.gz -target mean_initial.nii.gz -out subj_fa_combined.nii.gz Changed lines 70-78 from:
The computed inverse will be output as ''subj_aff_diffeo.df_inv.nii.gz''.
->3. combine the two inverted transformations with the command ''dfLeftComposeAffine'' (not ''dfRightComposeAffine'')
->[@
dfLeftComposeAffine -df subj_aff_diffeo.df_inv.nii.gz -aff subj_inv.aff -out subj_combined.df_inv.nii.gz
@]
The combined displacement field will be stored in ''subj_combined.df_inv.nii.gz''.
to:
->Note that you can compute the warped FA map of a subject DTI volume in two ways. One is to warp the DTI volume and then compute the FA map. Or you can first compute the FA map then warp the FA map. Many people in the DTI community argue that the former is preferred because the interpolation accounts for the tensorial properties. Changed lines 73-76 from:
!!!Mapping the atlas space data to the subject space (:showhide init=hide div=mapping_to_subject_space:)
>>id=mapping_to_subject_space padding=5px<<
The command to achieve this is the same as the ones described in the section on mapping the subject space data to the atlas space. Obviously, you will need to use the appropriate combined displacement from the template space to the native space of the subject data. This is useful for atlas-based segmentation in which you create some region definition in the atlas space then segment the corresponding region in the subject space by warping. The command will look like this
to:
!!!Combined displacement field from the template space to the native space (:showhide init=hide div=combined_displacement_template_to_native:)
>>id=combined_displacement_template_to_native padding=5px<<
Use the same example as the one above. We will compute the inverse of the affine transformation and that of the deformable transformation, then combine them appropriately. The steps are as follows:
->1. compute the inverse of the affine transformation with the command ''affine3Dtool''
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deformationScalarVolume -in roi_atlas.nii.gz -trans subj_combined.df_inv.nii.gz -target subj.nii.gz -interp 1 -out roi_subj_space.nii.gz
to:
affine3Dtool -in subj.aff -invert -out subj_inv.aff Changed lines 83-89 from:
where ''roi_atlas.nii.gz'' is some segmentation in the template space and the output ''roi_subj_space.nii.gz'' will be the same segmentation mapped onto the native space of ''subj.nii.gz''. The additional flag ''-interp'' is used to choose the nearest neighbor interpolation, rather than the default trilinear setting. This usually makes the most sense for propagating binary segmentations.
>><<
!!!Warping the images with affine transforms only (:showhide init=hide div=affine_warping:)
>>id=affine_warping padding=5px<<
The commands for warping scalar and tensor volumes are the ''affineScalarVolume'' and ''affineSymTensor3DVolume'', respectively. For scalar volumes, the typical usage is
to:
The computed inverse will be stored in ''subj_inv.aff''.
->2. compute the inverse of the deformable transformation with the command ''dfToInverse''
Changed line 88 from:
affineScalarVolume -in input.nii.gz -out output.nii.gz -trans input.aff -target reference.nii.gz
to:
dfToInverse -in subj_aff_diffeo.df.nii.gz Changed lines 91-94 from:
Most of the options are self-explanatory. The ''-target'' option serves the same purpose as the one described above. Additional options can be viewed with the ''-h'' option.
For tensor volumes, the typical usage is the same, which is
to:
The computed inverse will be output as ''subj_aff_diffeo.df_inv.nii.gz''.
->3. combine the two inverted transformations with the command ''dfLeftComposeAffine'' (not ''dfRightComposeAffine'')
Changed line 96 from:
affineSymTensor3DVolume -in input.nii.gz -out output.nii.gz -trans input.aff -target reference.nii.gz
to:
dfLeftComposeAffine -df subj_aff_diffeo.df_inv.nii.gz -aff subj_inv.aff -out subj_combined.df_inv.nii.gz Added lines 98-99:
The combined displacement field will be stored in ''subj_combined.df_inv.nii.gz''. Added lines 101-128:
!!!Mapping the atlas space data to the subject space (:showhide init=hide div=mapping_to_subject_space:)
>>id=mapping_to_subject_space padding=5px<<
The command to achieve this is the same as the ones described in the section on mapping the subject space data to the atlas space. Obviously, you will need to use the appropriate combined displacement from the template space to the native space of the subject data. This is useful for atlas-based segmentation in which you create some region definition in the atlas space then segment the corresponding region in the subject space by warping. The command will look like this
->[@
deformationScalarVolume -in roi_atlas.nii.gz -trans subj_combined.df_inv.nii.gz -target subj.nii.gz -interp 1 -out roi_subj_space.nii.gz
@]
where ''roi_atlas.nii.gz'' is some segmentation in the template space and the output ''roi_subj_space.nii.gz'' will be the same segmentation mapped onto the native space of ''subj.nii.gz''. The additional flag ''-interp'' is used to choose the nearest neighbor interpolation, rather than the default trilinear setting. This usually makes the most sense for propagating binary segmentations.
>><<
!!!Warping the images with affine transforms only (:showhide init=hide div=affine_warping:)
>>id=affine_warping padding=5px<<
The commands for warping scalar and tensor volumes are the ''affineScalarVolume'' and ''affineSymTensor3DVolume'', respectively. For scalar volumes, the typical usage is
->[@
affineScalarVolume -in input.nii.gz -out output.nii.gz -trans input.aff -target reference.nii.gz
@]
Most of the options are self-explanatory. The ''-target'' option serves the same purpose as the one described above. Additional options can be viewed with the ''-h'' option.
For tensor volumes, the typical usage is the same, which is
->[@
affineSymTensor3DVolume -in input.nii.gz -out output.nii.gz -trans input.aff -target reference.nii.gz
@]
>><<
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# '''Warping your DTI data to the template space with a different voxel size'''
to:
->'''Warping your DTI data to the template space with a different voxel size'''
Changed lines 48-51 from:
# '''A pair of convenient scripts for warping your DTI data to the template space'''
# '''Warping your scalar-valued data'''
to:
->'''A pair of convenient scripts for warping your DTI data to the template space'''
->'''Warping your scalar-valued data'''
Changed lines 42-45 from:
Often, we need the warped data in a voxel space with a different voxel size, i.e., to have higher spatial resolutions for subsequent analyses. This can be achieved by specifying the desired voxel size with the flag ''-vsize". For example, adding ''-vsize 1 1 1" to the command above will result in a warped volume with isotropic voxels of 1x1x1 mm^3.
There is a similar command for warping scalar volumes called ''deformationScalarVolume''. The example below shows how to warp the FA map of the same image with this command.
to:
'''Extra Goodies'''
# '''Warping your DTI data to the template space with a different voxel size'''
->Often, we need the warped data in a voxel space with a different voxel size, i.e., to have higher spatial resolutions for subsequent analyses. This can be achieved by specifying the desired voxel size with the flag ''-vsize". For example, adding ''-vsize 1 1 1" to the command above will result in a warped volume with isotropic voxels of 1x1x1 mm^3.
# '''A pair of convenient scripts for warping your DTI data to the template space'''
# '''Warping your scalar-valued data'''
->There is a similar command for warping scalar volumes called ''deformationScalarVolume''. The example below shows how to warp the FA map of the same image with this command.
Changed line 58 from:
Note that you can compute the warped FA map of a subject DTI volume in two ways. One is to warp the DTI volume and then compute the FA map. Or you can first compute the FA map then warp the FA map. Many people in the DTI community argue that the former is preferred because the interpolation accounts for the tensorial properties. to:
->Note that you can compute the warped FA map of a subject DTI volume in two ways. One is to warp the DTI volume and then compute the FA map. Or you can first compute the FA map then warp the FA map. Many people in the DTI community argue that the former is preferred because the interpolation accounts for the tensorial properties.
Changed line 4 from:
to:
Changed line 19 from:
!!Combined displacement field from the native space to the template space (:showhide init=hide div=combined_displacement_native_to_template:) to:
!!!Combined displacement field from the native space to the template space (:showhide init=hide div=combined_displacement_native_to_template:) Changed line 32 from:
!!Mapping the subject data to the template space (:showhide init=hide div=mapping_to_template_space:) to:
!!!Mapping the subject data to the template space (:showhide init=hide div=mapping_to_template_space:) Changed line 53 from:
!!Combined displacement field from the template space to the native space (:showhide init=hide div=combined_displacement_template_to_native:) to:
!!!Combined displacement field from the template space to the native space (:showhide init=hide div=combined_displacement_template_to_native:) Changed line 82 from:
!!Mapping the atlas space data to the subject space (:showhide init=hide div=mapping_to_subject_space:) to:
!!!Mapping the atlas space data to the subject space (:showhide init=hide div=mapping_to_subject_space:) Changed line 93 from:
!!Warping the images with affine transforms only (:showhide init=hide div=affine_warping:) to:
!!!Warping the images with affine transforms only (:showhide init=hide div=affine_warping:)
Changed lines 19-20 from:
!!Combined displacement field from the native space to the template space (:showhide init=hide div=combined_displacement:)
>>id=combined_displacement padding=5px<< to:
!!Combined displacement field from the native space to the template space (:showhide init=hide div=combined_displacement_native_to_template:)
>>id=combined_displacement_native_to_template padding=5px<< Changed lines 53-54 from:
!!Combined displacement field from the template space to the native space to:
!!Combined displacement field from the template space to the native space (:showhide init=hide div=combined_displacement_template_to_native:)
>>id=combined_displacement_template_to_native padding=5px<< Changed lines 80-81 from:
!!Mapping the atlas space data to the subject space to:
>><<
!!Mapping the atlas space data to the subject space (:showhide init=hide div=mapping_to_subject_space:)
>>id=mapping_to_subject_space padding=5px<< Changed lines 91-92 from:
!!Warping the images with affine transforms only to:
>><<
!!Warping the images with affine transforms only (:showhide init=hide div=affine_warping:)
>>id=affine_warping padding=5px<< Changed lines 107-108 from:
to:
Changed lines 32-33 from:
!!Mapping the subject data to the template space to:
!!Mapping the subject data to the template space (:showhide init=hide div=mapping_to_template_space:)
>>id=mapping_to_template_space padding=5px<< Changed lines 51-52 from:
to:
Changed lines 19-20 from:
!!Combined displacement field from the native space to the template space to:
!!Combined displacement field from the native space to the template space (:showhide init=hide div=combined_displacement:)
>>id=combined_displacement padding=5px<< Changed lines 30-31 from:
to:
Changed lines 71-73 from:
dfLeftComposeAffine -df subj_aff_diffeo.df_inv.nii.gz -aff subj_inv.aff -out subj_combined.df_inv.nii.gz @] to:
dfLeftComposeAffine -df subj_aff_diffeo.df_inv.nii.gz -aff subj_inv.aff -out subj_combined.df_inv.nii.gz
@]
Changed lines 15-19 from:
In addition, we will also describe how
# to warp images with the affine transform only;
# to warp images to voxel sizes different from the target volume.
to:
In addition, we will also describe how to
# warp images with the affine transform only;
# warp images to voxel sizes different from the target volume.
Changed line 9 from:
Two common needs arise here: to:
Two common needs arise here: Changed lines 11-15 from:
# to warp the template to the native space of a particular subject with a single interpolation operation. Meeting these needs require the ability to combine the affine transformation and the displacement field into one single displacement field, as well as the ability to invert this single displacement field. This tutorial will describe the procedure to accomplish these goals.
In addition, we will describe how to warp images with the affine transform only.
to:
# to warp the template to the native space of a particular subject with a single interpolation operation.
Meeting these needs require the ability to combine the affine transformation and the displacement field into one single displacement field, as well as the ability to invert this single displacement field. This tutorial will describe the procedure to accomplish these goals.
In addition, we will also describe how
# to warp images with the affine transform only;
# to warp images to voxel sizes different from the target volume.
Added lines 40-41:
Often, we need the warped data in a voxel space with a different voxel size, i.e., to have higher spatial resolutions for subsequent analyses. This can be achieved by specifying the desired voxel size with the flag ''-vsize". For example, adding ''-vsize 1 1 1" to the command above will result in a warped volume with isotropic voxels of 1x1x1 mm^3.
Changed line 73 from:
deformationScalarVolume -in roi_atlas.nii.gz -trans subj_combined.df_inv.nii.gz -target subj.nii.gz -out roi_subj_space.nii.gz to:
deformationScalarVolume -in roi_atlas.nii.gz -trans subj_combined.df_inv.nii.gz -target subj.nii.gz -interp 1 -out roi_subj_space.nii.gz Changed lines 75-76 from:
where ''roi_atlas.nii.gz'' is some segmentation in the template space and the output ''roi_subj_space.nii.gz'' will be the same segmentation mapped onto the native space of ''subj.nii.gz''.
to:
where ''roi_atlas.nii.gz'' is some segmentation in the template space and the output ''roi_subj_space.nii.gz'' will be the same segmentation mapped onto the native space of ''subj.nii.gz''. The additional flag ''-interp'' is used to choose the nearest neighbor interpolation, rather than the default trilinear setting. This usually makes the most sense for propagating binary segmentations.
Changed line 90 from:
to:
Changed line 39 from:
deformationScalarVolume -in subj_fa.nii.gz -trans subj_combined.df.nii.gz -target mean_initial.nii.gz out subj_fa_combined.nii.gz to:
deformationScalarVolume -in subj_fa.nii.gz -trans subj_combined.df.nii.gz -target mean_initial.nii.gz -out subj_fa_combined.nii.gz
Changed line 1 from:
(:noleft:) (:notitle:)(:title Options:) to:
(:noleft:) (:notitle:)(:title DTI-TK:Documentation:Image Mapping Options After Registration:)
Changed lines 19-20 from:
->[@ dfRightComposeAffine -aff subj.aff -df subj_aff_diffeo.df.nii.gz -out subj_combined.df.nii.gz to:
->[@
dfRightComposeAffine -aff subj.aff -df subj_aff_diffeo.df.nii.gz -out subj_combined.df.nii.gz
Changed lines 29-30 from:
-> [@ deformationSymTensor3DVolume -in subj.nii.gz -trans subj_combined.df.nii.gz -target mean_initial.nii.gz -out subj_combined.nii.gz to:
-> [@
deformationSymTensor3DVolume -in subj.nii.gz -trans subj_combined.df.nii.gz -target mean_initial.nii.gz -out subj_combined.nii.gz Changed lines 37-38 from:
->[@ deformationScalarVolume -in subj_fa.nii.gz -trans subj_combined.df.nii.gz -target mean_initial.nii.gz out subj_fa_combined.nii.gz to:
->[@
deformationScalarVolume -in subj_fa.nii.gz -trans subj_combined.df.nii.gz -target mean_initial.nii.gz out subj_fa_combined.nii.gz Changed lines 46-48 from:
->1. compute the inverse of the affine transformation with the command affine3DInvert
->[@ affine3DInvert subj.aff subj_inv.aff to:
->1. compute the inverse of the affine transformation with the command ''affine3Dtool''
->[@
affine3Dtool -in subj.aff -invert -out subj_inv.aff Changed lines 54-56 from:
->2. compute the inverse of the deformable transformation with the command dfToInverse
->[@ dfToInverse -in subj_aff_diffeo.df.nii.gz to:
->2. compute the inverse of the deformable transformation with the command ''dfToInverse''
->[@
dfToInverse -in subj_aff_diffeo.df.nii.gz Changed lines 60-66 from:
The computed inverse will be output as subj_aff_diffeo.df_inv.nii.gz.
->3. combine the two inverted transformations with the command dfLeftComposeAffine (not dfRightComposeAffine)
->[@ dfLeftComposeAffine -df subj_aff_diffeo.df_inv.nii.gz -aff subj_inv.aff -out subj_combined.df_inv.nii.gz @]
The combined displacement field will be stored in subj_combined.df_inv.nii.gz.
to:
The computed inverse will be output as ''subj_aff_diffeo.df_inv.nii.gz''.
->3. combine the two inverted transformations with the command ''dfLeftComposeAffine'' (not ''dfRightComposeAffine'')
->[@
dfLeftComposeAffine -df subj_aff_diffeo.df_inv.nii.gz -aff subj_inv.aff -out subj_combined.df_inv.nii.gz @]
The combined displacement field will be stored in ''subj_combined.df_inv.nii.gz''.
Changed lines 71-72 from:
->[@ deformationScalarVolume -in roi_atlas.nii.gz -trans subj_combined.df_inv.nii.gz -target subj.nii.gz -out roi_subj_space.nii.gz to:
->[@
deformationScalarVolume -in roi_atlas.nii.gz -trans subj_combined.df_inv.nii.gz -target subj.nii.gz -out roi_subj_space.nii.gz Changed lines 74-75 from:
where roi_atlas.nii.gz is some segmentation in the template space and the output roi_subj_space.nii.gz will be the same segmentation mapped onto the native space of subj.nii.gz.
to:
where ''roi_atlas.nii.gz'' is some segmentation in the template space and the output ''roi_subj_space.nii.gz'' will be the same segmentation mapped onto the native space of ''subj.nii.gz''.
Changed lines 77-79 from:
The commands for warping scalar and tensor volumes are the affineScalarVolume and affineSymTensor3DVolume, respectively. For scalar volumes, the typical usage is
->[@ affineScalarVolume -in input.nii.gz -out output.nii.gz -trans input.aff -target reference.nii.gz to:
The commands for warping scalar and tensor volumes are the ''affineScalarVolume'' and ''affineSymTensor3DVolume'', respectively. For scalar volumes, the typical usage is
->[@
affineScalarVolume -in input.nii.gz -out output.nii.gz -trans input.aff -target reference.nii.gz Changed lines 87-88 from:
->[@ affineSymTensor3DVolume -in input.nii.gz -out output.nii.gz -trans input.aff -target reference.nii.gz
@] to:
->[@
affineSymTensor3DVolume -in input.nii.gz -out output.nii.gz -trans input.aff -target reference.nii.gz
@]
Added lines 4-15:
!!Overview
After the registration/spatial normalization step, DTI-TK outputs, for each subject, two transformations that together defines the mapping from the subject to the template space:
# the affine transformation stored in a text file with suffix ''aff'', which minimizes the global difference between the subject and the template, and
# the displacement field stored in a NIfTI formatted vector volume with suffix ''df.nii.gz'', which minimizes the residual local difference between the subject and the template.
Two common needs arise here:
# to warp the subject data in its native space to the template space with a single interpolation operation;
# to warp the template to the native space of a particular subject with a single interpolation operation. Meeting these needs require the ability to combine the affine transformation and the displacement field into one single displacement field, as well as the ability to invert this single displacement field. This tutorial will describe the procedure to accomplish these goals.
In addition, we will describe how to warp images with the affine transform only.
Changed line 24 from:
->[@ deformationScalarVolume -in subj_fa.nii.gz -trans subj_combined.df.nii.gz -target mean_initial.nii.gz -out subj_fa_combined.nii.gz to:
->[@ deformationScalarVolume -in subj_fa.nii.gz -trans subj_combined.df.nii.gz -target mean_initial.nii.gz out subj_fa_combined.nii.gz Changed lines 29-30 from:
Combined displacement field from the template space to the native space
to:
!!Combined displacement field from the template space to the native space Changed lines 37-38 from:
The computed inverse will be stored in subj_inv.aff.
to:
The computed inverse will be stored in ''subj_inv.aff''.
Added line 43:
Changed lines 48-49 from:
->[@ dfLeftComposeAffine -df subj_aff_diffeo.df_inv.nii.gz -aff subj_inv.aff -out subj_combined.df_inv.nii.gz
@] to:
->[@ dfLeftComposeAffine -df subj_aff_diffeo.df_inv.nii.gz -aff subj_inv.aff -out subj_combined.df_inv.nii.gz @] Deleted line 50:
Changed lines 54-55 from:
->[@ deformationScalarVolume -in roi_atlas.nii.gz -trans subj_combined.df_inv.nii.gz -target subj.nii.gz -out
roi_subj_space.nii.gz to:
->[@ deformationScalarVolume -in roi_atlas.nii.gz -trans subj_combined.df_inv.nii.gz -target subj.nii.gz -out roi_subj_space.nii.gz Added line 63:
Added line 67:
Added lines 1-70:
(:noleft:) (:notitle:)(:title Options:)
! Image mapping options after registration
!!Combined displacement field from the native space to the template space
Recall that when registering some subject data with the filename ''subj.nii.gz'', the output affine transformation file will be subj.aff and the output displacement field will be ''subj_aff_diffeo.df.nii.gz''. The command to combine these two transformations is ''dfRightComposeAffine''
->[@ dfRightComposeAffine -aff subj.aff -df subj_aff_diffeo.df.nii.gz -out subj_combined.df.nii.gz
@]
The combined displacement field will be stored in ''subj_combined.df.nii.gz''.The diagram below illustrates the relationship between all the transformations and images.
%center%Attach:dtitk_mapping_subject_to_template.png
!!Mapping the subject data to the template space
During the registration/normalization step, the subject data ''subj.nii.gz'' will be first warped by the affine transformation to produce ''subj_aff.nii.gz'', which will be subsequently warped by the deformable transformation to produce subj_aff_diffeo.nii.gz. Evidently, the two steps require two image interpolation/resampling operations. Using the combined displacement field we have just computed above, we can map the subject data directly to the template space with a single interpolation operation. This is usually more desirable to minimize the smoothing effect of interpolation. This is achieved with the command ''deformationSymTensor3DVolume''.
-> [@ deformationSymTensor3DVolume -in subj.nii.gz -trans subj_combined.df.nii.gz -target mean_initial.nii.gz -out subj_combined.nii.gz
@]
The option ''-target'' allows you to specify the desired voxel space to output the warped data. In our example, the warped data will have the same voxel space as ''mean_initial.nii.gz''. You can provide a different image with a different voxel space as you wish, e.g., to output the warped image at a lower or higher spatial resolution.
There is a similar command for warping scalar volumes called ''deformationScalarVolume''. The example below shows how to warp the FA map of the same image with this command.
->[@ deformationScalarVolume -in subj_fa.nii.gz -trans subj_combined.df.nii.gz -target mean_initial.nii.gz -out subj_fa_combined.nii.gz
@]
Note that you can compute the warped FA map of a subject DTI volume in two ways. One is to warp the DTI volume and then compute the FA map. Or you can first compute the FA map then warp the FA map. Many people in the DTI community argue that the former is preferred because the interpolation accounts for the tensorial properties.
Combined displacement field from the template space to the native space
Use the same example as the one above. We will compute the inverse of the affine transformation and that of the deformable transformation, then combine them appropriately. The steps are as follows:
->1. compute the inverse of the affine transformation with the command affine3DInvert
->[@ affine3DInvert subj.aff subj_inv.aff
@]
The computed inverse will be stored in subj_inv.aff.
->2. compute the inverse of the deformable transformation with the command dfToInverse
->[@ dfToInverse -in subj_aff_diffeo.df.nii.gz
@]
The computed inverse will be output as subj_aff_diffeo.df_inv.nii.gz.
->3. combine the two inverted transformations with the command dfLeftComposeAffine (not dfRightComposeAffine)
->[@ dfLeftComposeAffine -df subj_aff_diffeo.df_inv.nii.gz -aff subj_inv.aff -out subj_combined.df_inv.nii.gz
@]
The combined displacement field will be stored in subj_combined.df_inv.nii.gz.
!!Mapping the atlas space data to the subject space
The command to achieve this is the same as the ones described in the section on mapping the subject space data to the atlas space. Obviously, you will need to use the appropriate combined displacement from the template space to the native space of the subject data. This is useful for atlas-based segmentation in which you create some region definition in the atlas space then segment the corresponding region in the subject space by warping. The command will look like this
->[@ deformationScalarVolume -in roi_atlas.nii.gz -trans subj_combined.df_inv.nii.gz -target subj.nii.gz -out
roi_subj_space.nii.gz
@]
where roi_atlas.nii.gz is some segmentation in the template space and the output roi_subj_space.nii.gz will be the same segmentation mapped onto the native space of subj.nii.gz.
!!Warping the images with affine transforms only
The commands for warping scalar and tensor volumes are the affineScalarVolume and affineSymTensor3DVolume, respectively. For scalar volumes, the typical usage is
->[@ affineScalarVolume -in input.nii.gz -out output.nii.gz -trans input.aff -target reference.nii.gz
@]
Most of the options are self-explanatory. The ''-target'' option serves the same purpose as the one described above. Additional options can be viewed with the ''-h'' option.
For tensor volumes, the typical usage is the same, which is
->[@ affineSymTensor3DVolume -in input.nii.gz -out output.nii.gz -trans input.aff -target reference.nii.gz
@]
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