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Documentation.Registration History
Hide minor edits - Show changes to output
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dti_diffeomorphic_population mean_affine3.nii.gz subjs_aff.txt mask.nii.gz 0.002
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Really important to check that the mask is appropriate before embarking on the next most time-consuming step. Make sure none of the voxels in the top two and bottom two slices fall within the mask. If this is not the case, please use software like [[http://itksnap.org | ITK-SNAP]] to edit the mask to meet the requirement.
-> [@
dti_diffeomorphic_population mean_affine3.nii.gz subjs_aff.txt mask.nii.gz 0.002
@]
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'''Caution''': Check that the mask image produced makes sense. The mask image should have '''a value of 1 for the voxels within the brain parenchyma''' and '''0 outside'''. Make sure that none of the voxels in the top two and bottom two slices take the value 1. If this is not the case, please use software like [[http://itksnap.org ITK-SNAP]] to edit the mask to meet the requirement.
to:
'''Caution''': Check that the mask image produced makes sense. The mask image should have '''a value of 1 for the voxels within the brain parenchyma''' and '''0 outside'''. Make sure that none of the voxels in the top two and bottom two slices take the value 1. If this is not the case, please use software like [[http://itksnap.org | ITK-SNAP]] to edit the mask to meet the requirement.
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'''Caution''': Check that the mask image produced makes sense. The mask image should have '''a value of 1 for the voxels within the brain parenchyma''' and '''0 outside'''.
to:
'''Caution''': Check that the mask image produced makes sense. The mask image should have '''a value of 1 for the voxels within the brain parenchyma''' and '''0 outside'''. Make sure that none of the voxels in the top two and bottom two slices take the value 1. If this is not the case, please use software like [[http://itksnap.org ITK-SNAP]] to edit the mask to meet the requirement.
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TVtool -in tensor.nii.gz -tr to:
TVtool -in template.nii.gz -tr
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'''Caution''': Check that the mask image produced make sense. The mask should assign '''a value of 1 for the voxels within the brain parenchyma''' and '''0 outside'''.
to:
'''Caution''': Check that the mask image produced makes sense. The mask image should have '''a value of 1 for the voxels within the brain parenchyma''' and '''0 outside'''.
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'''Caution''': Check that the mask image produced make sense. The mask should assign '''a value of 1 for the voxels within the brain parenchyma''' and '''0 outside'''.
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*For human subjects (10 years old or older), the template that serves this purpose well is the [[http://www.nitrc.org/frs/download.php/2306/ixi_aging_template_v2.0.tgz| IXI aging template]]. You may wonder why an aging template can be used for subjects with a much broader age range. This is because it is used to serve a very restricted role: to ensure that our final template is located and oriented in space in a manner consistent with the standard template spaces, such as MNI. It will not have any influence on the size and the shape of the final template. to:
*For human subjects (10 years old or older), the template that serves this purpose well is the [[http://www.nitrc.org/frs/download.php/5518/ixi_aging_template_v3.0.tgz| IXI aging template]]. You may wonder why an aging template can be used for subjects with a much broader age range. This is because it is used to serve a very restricted role: to ensure that our final template is located and oriented in space in a manner consistent with the standard template spaces, such as MNI. It will not have any influence on the size and the shape of the final template. Changed line 217 from:
%center%Attach:atlas_example.png to:
%center%Attach:atlas_example.png
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On this page, we will first go through each of these steps in detail. A practical example with illustrations is given at the very end of it. Be sure to check that out!
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On this page, we will first go through each of these steps in detail.
A '''practical example''' with illustrations is given at the very end of the tutorial. This example is a '''must read'''. It gives all the steps that you need in most standard scenarios.
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# An existing tensor template. For human subjects (10 years old or older), the template that serves this purpose well is the [[http://www.nitrc.org/frs/download.php/2306/ixi_aging_template_v2.0.tgz| IXI aging template]]. The installation of the template is straightforward: just move the ''.tgz'' package to a directory of your choice and uncompress it. The template we need is under the ''template'' directory and called ''ixi_aging_template.nii.gz''. In the example command below, the directory I used to uncompress the template is /home/huiz.
'''Why should I use an aging template for my adult population?''': The short answer is that this is '''NOT''' a concern for the present purpose. We are using the IXI aging template for a very restricted purpose: to ensure that our final template is located and oriented in space in a manner consistent with the standard template spaces, such as MNI. It will not have any influence on the size and the shape of the final template.
# A text file with a list of the filenames of the subject volumes, in the same directory as the subject volumes (see [[Attach:subjs.txt|here]] for example). Make sure the files with the ''nii.gz'' suffix. In the example command below, the text file is named subjs.txt.
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#A text file with a list of the filenames of the subject volumes, in the same directory as the subject volumes (see [[Attach:subjs.txt|here]] for example). Make sure the files with the ''nii.gz'' suffix. In the example command below, the text file is named subjs.txt.
#An existing tensor template.
*For human subjects (10 years old or older), the template that serves this purpose well is the [[http://www.nitrc.org/frs/download.php/2306/ixi_aging_template_v2.0.tgz| IXI aging template]]. You may wonder why an aging template can be used for subjects with a much broader age range. This is because it is used to serve a very restricted role: to ensure that our final template is located and oriented in space in a manner consistent with the standard template spaces, such as MNI. It will not have any influence on the size and the shape of the final template.
*The installation of the template is straightforward: just move the ''.tgz'' package to a directory of your choice and uncompress it. The template we need is under the ''template'' directory and called ''ixi_aging_template.nii.gz''. In the example command below, the directory I used to uncompress the template is /home/huiz.
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'''Why should I use an aging template for my adult population?''': The short answer is that this is '''NOT''' a concern for the present purpose. We are using the IXI aging template for a very restricted purpose: to ensure that our final template is located and oriented in space in a manner consistent with the standard template spaces, such as MNI. It will not have any influence on the size and the shape of the final template.
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'''Why should I use an aging template for my adult population?''': The short answer is that this is '''NOT''' a concern for the present purpose. We are using the IXI aging template for a very restricted purpose: to ensure that our final template is located and oriented in space in a manner consistent with the standard template spaces, such as MNI. It will not have any influence on the size and the shape of the final template.
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'''Why should I use an aging template for my adult population?''': The short answer is that this is '''NOT''' a concern for the present purpose. We are using the IXI aging template for a very restricted purpose: to ensure that our final template is located and oriented in space in a manner consistent with the standard template spaces, such as MNI. It will not have any influence on the size and the shape of the final template.
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