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Documentation.TBSS History
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'''NEW''': A recent NeuroImage article entitled [[http://www.sciencedirect.com/science/article/pii/S1053811914004984 | Methodological considerations on tract-based spatial statistics (TBSS)]] recommends the use of DTI-TK to enhance TBSS.
to:
'''Update (August 2014)''': A recent NeuroImage article entitled [[http://www.sciencedirect.com/science/article/pii/S1053811914004984 | Methodological considerations on tract-based spatial statistics (TBSS)]] recommends the use of DTI-TK to enhance TBSS.
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'''NEW''': A recent NeuroImage article entitled [[http://www.sciencedirect.com/science/article/pii/S1053811914004984 | Methodological considerations on tract-based spatial statistics (TBSS)]] recommends the use of DTI-TK to enhance TBSS.
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After completing this custom @@tbss_3_postreg@@, simply change to the directory of @@tbss@@, which you just created, and continue with the final two steps in TBSS. to:
After completing this custom @@tbss_3_postreg@@, simply change to the directory of @@tbss@@, which you just created, and continue with the final two steps in TBSS.
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->You can use TVtool as above but applied to all the spatially normalized high-resolution DTI data from above. Subsequently, use @@fslmerge@@ to combine them into a 4-D volume called @@all_FA@@.
to:
->You can use TVtool as above but applied to all the spatially normalized high-resolution DTI data from above. Subsequently, use @@fslmerge@@ to combine them into a 4-D volume called @@all_FA@@. Finally, apply @@fslmaths@@ to @@all_FA@@ to create a combined binary mask volume called @@mean_FA_mask@@. The command to do this
->[@
fslmaths all_FA -max 0 -Tmin -bin mean_FA_mask -odt char
@]
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->Create a directory called @@tbss@@ with a subdirectory called @@stats@@. Copy @@mean_FA_skeleton@@ and @@all_FA@@ to the @@stats@@ subdirectory.
to:
->Create a directory called @@tbss@@ with a subdirectory called @@stats@@. Copy @@mean_FA_skeleton@@, @@all_FA@@, and @@mean_FA_mask@@ to the @@stats@@ subdirectory.
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The integration of DTI-TK output into the TBSS pipeline requires a '''custom implementation of tbss_3_postreg''', the goal of which is to generate the spatially normalized high-resolution DTI data, i.e., with a spatial resolution of isotropic 1mm'^3^', the mean FA skeleton, and the 4-D FA map of the spatially normalized high-resolution DTI data. (:showhide init=hide div=tbss_3_postreg:) to:
The integration of DTI-TK output into the TBSS pipeline requires a '''custom implementation of @@tbss_3_postreg@@''', the goal of which is to generate the spatially normalized high-resolution DTI data, i.e., with a spatial resolution of isotropic 1mm'^3^', the mean FA skeleton, and the 4-D FA map of the spatially normalized high-resolution DTI data. (:showhide init=hide div=tbss_3_postreg:)
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As outlined in the TBSS documentation, there are altogether six components to the full analysis: '''0)''' ''Preprocessing'', '''1)''' ''tbss_1_preproc'', '''2)''' ''tbss_2_reg'', '''3)''' ''tbss_3_postreg'', '''4)''' ''tbss_4_prestats'', and '''5)''' ''stats''.
to:
As outlined in the TBSS documentation, there are altogether six components to the full analysis: '''0)''' @@Preprocessing@@, '''1)''' @@tbss_1_preproc@@, '''2)''' @@tbss_2_reg@@, '''3)''' @@tbss_3_postreg@@, '''4)''' @@tbss_4_prestats@@, and '''5)''' @@stats@@.
Changed line 68 from:
After completing this custom tbss_3_postreg, simply change to the directory of @@tbss@@, which you just created, and continue with the final two steps in TBSS. to:
After completing this custom @@tbss_3_postreg@@, simply change to the directory of @@tbss@@, which you just created, and continue with the final two steps in TBSS.
Added line 68:
After completing this custom tbss_3_postreg, simply change to the directory of @@tbss@@, which you just created, and continue with the final two steps in TBSS.
Changed lines 14-16 from:
The integration of DTI-TK output into the TBSS pipeline requires:
1) custom implementation of tbss_3_postreg''', the goal of which is to generate the spatially normalized high-resolution DTI data, i.e., with a spatial resolution of isotropic 1mm'^3^', the mean FA skeleton, and the 4-D FA map of the spatially normalized high-resolution DTI data. (:showhide init=hide div=tbss_3_postreg:) to:
The integration of DTI-TK output into the TBSS pipeline requires a '''custom implementation of tbss_3_postreg''', the goal of which is to generate the spatially normalized high-resolution DTI data, i.e., with a spatial resolution of isotropic 1mm'^3^', the mean FA skeleton, and the 4-D FA map of the spatially normalized high-resolution DTI data. (:showhide init=hide div=tbss_3_postreg:)
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'''custom implementation of tbss_3_postreg''', the goal of which is to generate the spatially normalized high-resolution DTI data, i.e., with a spatial resolution of isotropic 1mm'^3^', the mean FA skeleton, and the 4-D FA map of the spatially normalized high-resolution DTI data. (:showhide init=hide div=tbss_3_postreg:) to:
'''1) custom implementation of tbss_3_postreg''', the goal of which is to generate the spatially normalized high-resolution DTI data, i.e., with a spatial resolution of isotropic 1mm'^3^', the mean FA skeleton, and the 4-D FA map of the spatially normalized high-resolution DTI data. (:showhide init=hide div=tbss_3_postreg:)
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* '''custom implementation of tbss_3_postreg''', the goal of which is to generate the spatially normalized high-resolution DTI data, i.e., with a spatial resolution of isotropic 1mm'^3^', the mean FA skeleton, and the 4-D FA map of the spatially normalized high-resolution DTI data. (:showhide init=hide div=tbss_3_postreg:)
to:
'''custom implementation of tbss_3_postreg''', the goal of which is to generate the spatially normalized high-resolution DTI data, i.e., with a spatial resolution of isotropic 1mm'^3^', the mean FA skeleton, and the 4-D FA map of the spatially normalized high-resolution DTI data. (:showhide init=hide div=tbss_3_postreg:)
Changed line 16 from:
First, a '''custom implementation of tbss_3_postreg''', the goal of which is to generate the spatially normalized high-resolution DTI data, i.e., with a spatial resolution of isotropic 1mm'^3^', the mean FA skeleton, and the 4-D FA map of the spatially normalized high-resolution DTI data. (:showhide init=hide div=tbss_3_postreg:)
to:
* '''custom implementation of tbss_3_postreg''', the goal of which is to generate the spatially normalized high-resolution DTI data, i.e., with a spatial resolution of isotropic 1mm'^3^', the mean FA skeleton, and the 4-D FA map of the spatially normalized high-resolution DTI data. (:showhide init=hide div=tbss_3_postreg:)
Changed line 16 from:
First, a custom implementation of the fourth step '''tbss_3_postreg''', the goal of which is to generate the spatially normalized high-resolution DTI data, i.e., with a spatial resolution of isotropic 1mm'^3^', the mean FA skeleton, and the 4-D FA map of the spatially normalized high-resolution DTI data. (:showhide init=hide div=tbss_3_postreg:) to:
First, a '''custom implementation of tbss_3_postreg''', the goal of which is to generate the spatially normalized high-resolution DTI data, i.e., with a spatial resolution of isotropic 1mm'^3^', the mean FA skeleton, and the 4-D FA map of the spatially normalized high-resolution DTI data. (:showhide init=hide div=tbss_3_postreg:)
Changed lines 14-20 from:
The integration of DTI-TK output into the TBSS pipeline requires a custom implementation of the fourth step '''tbss_3_postreg'''. The goal is to
* generate the spatially normalized high-resolution DTI data, i.e., with a spatial resolution of isotropic 1mm'^3^'.
* generate the mean FA skeleton
* generate
(:showhide init=hide div=tbss_3_postreg:) to:
The integration of DTI-TK output into the TBSS pipeline requires:
First, a custom implementation of the fourth step '''tbss_3_postreg''', the goal of which is to generate the spatially normalized high-resolution DTI data, i.e., with a spatial resolution of isotropic 1mm'^3^', the mean FA skeleton, and the 4-D FA map of the spatially normalized high-resolution DTI data. (:showhide init=hide div=tbss_3_postreg:)
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!!Overview of the procedures
to:
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!!Custom implementation of tbss_3_postreg (:showhide init=hide div=tbss_3_postreg:)
to:
(:showhide init=hide div=tbss_3_postreg:)
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>>id=getting_started padding=5px<<
to:
>>id=tbss_3_postreg padding=5px<<
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!!Custom implementation of tbss_3_postreg
to:
!!Custom implementation of tbss_3_postreg (:showhide init=hide div=tbss_3_postreg:)
>>id=getting_started padding=5px<<
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to:
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->You can use TVtool as above but applied to all the spatially normalized high-resolution DTI data from above.
to:
->You can use TVtool as above but applied to all the spatially normalized high-resolution DTI data from above. Subsequently, use @@fslmerge@@ to combine them into a 4-D volume called @@all_FA@@.
* Place the TBSS relevant files into a folder that TBSS expects
->Create a directory called @@tbss@@ with a subdirectory called @@stats@@. Copy @@mean_FA_skeleton@@ and @@all_FA@@ to the @@stats@@ subdirectory.
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* generate the spatially normalized DTI data with a spatial resolution of isotropic 1mm'^3^'. to:
* generate the spatially normalized high-resolution DTI data, i.e., with a spatial resolution of isotropic 1mm'^3^'. Changed lines 18-19 from:
to:
* generate the 4-D FA map of the spatially normalized high-resolution DTI data.
Changed lines 62-65 from:
->'''IMPORTANT''': Make sure you visually verify the output skeleton in FSL. You should notice that there will be a ring on the edge of the brain. You don't see this with the standard TBSS because the '''tbss_1_preproc''' erodes the subject FA map slightly. My recommendation is not to modify the subject data this way. Instead, we clean the skeleton instead.
to:
->'''IMPORTANT''': Make sure you visually verify the output skeleton in FSL. You may notice that a ring around the edge of the brain. You can mask out this ring as a post-processing step or only worry about it after the final statistical analysis, i.e., ignore any significant findings along this ring.
* Generate the FA map of the spatially normalized high-resolution DTI data
->You can use TVtool as above but applied to all the spatially normalized high-resolution DTI data from above.
Added lines 61-64:
->'''IMPORTANT''': Make sure you visually verify the output skeleton in FSL. You should notice that there will be a ring on the edge of the brain. You don't see this with the standard TBSS because the '''tbss_1_preproc''' erodes the subject FA map slightly. My recommendation is not to modify the subject data this way. Instead, we clean the skeleton instead.
Changed lines 35-37 from:
->@@subjs_normalized.txt@@ is an ASCII text file that contains a list of the file names of the normalized high resolution DTI volumes from the previous step. @@mean_final_high_res.nii.gz@@ will be the output high resolution DTI template.
to:
->@@subjs_normalized.txt@@ is an ASCII text file that contains a list of the file names of the normalized high-resolution DTI volumes from the previous step. @@mean_final_high_res.nii.gz@@ will be the output high-resolution DTI template.
* Generate the FA map of the high-resolution population-specific DTI template
->[@
TVtool -in mean_final_high_res.nii.gz -fa
@]
* Rename the FA map to be consistent with the TBSS pipeline
->[@
mv mean_final_high_res_fa.nii.gz mean_FA.nii.gz
@]
->@@mean_FA.nii.gz@@ is now the new name for the high-resolution FA map of the DTI template.
* Generate the white matter skeleton from the high-resolution FA map of the DTI template
->'''Note''': This step requires that FSL is properly installed on your system, as we are going to need a tool from FSL.
->[@
tbss_skeleton -i mean_FA -o mean_FA_skeleton
@]
->@@mean_FA_skeleton@@ will be the white matter skeleton for running the subsequent TBSS analysis. The suffix (hdr/img or nii or nii.gz) depends on your FSL output configuration.
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->Here is an example command:
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->@@subjs.txt@@ is an ASCII text file that stores the list of the subject DTI volumes in their native space (after the DTI-TK pre-processing steps) and @@mean_final.nii.gz@@ is the final population-specific DTI template for these subjects computed with DTI-TK. This command should be executed while your current working directory is the directory where you have run all your DTI-TK registration steps.
to:
->@@subjs.txt@@ is an ASCII text file that contains a list of the file names of the subject DTI volumes in their native space (after the DTI-TK pre-processing steps) and @@mean_final.nii.gz@@ is the final population-specific DTI template for these subjects computed with DTI-TK. The last 3 arguments, not surprisingly, specify the desired voxel spacings. This command should be executed while your current working directory is the directory where you have run all your DTI-TK registration steps.
* Generate the population-specific DTI template with the isotropic 1mm'^3^' spacing.
->[@
TVMean -in subjs_normalized.txt -out mean_final_high_res.nii.gz
@]
->@@subjs_normalized.txt@@ is an ASCII text file that contains a list of the file names of the normalized high resolution DTI volumes from the previous step. @@mean_final_high_res.nii.gz@@ will be the output high resolution DTI template.
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->For example, if `subjs.txt`
to:
->Here is an example command:
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->@@subjs.txt@@ is an ASCII text file that stores the list of the subject DTI volumes in their native space (after the DTI-TK pre-processing steps) and @@mean_final.nii.gz@@ is the final population-specific DTI template for these subjects computed with DTI-TK. This command should be executed while your current working directory is the directory where you have run all your DTI-TK registration steps.
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to:
->For example, if `subjs.txt`
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* Generate the spatially normalized DTI data with the isotropic 1mm'^3^' resolution.
->For example
->[@
dti_warp_to_template_group subjs.txt mean_final.nii.gz 1 1 1
@]
Changed lines 10-11 from:
As outlined in the TBSS documentation, there are altogether six components to the full analysis: '''0)''' Preprocessing, '''1)''' tbss_1_preproc, '''2)''' tbss_2_reg, '''3)''' tbss_3_postreg, '''4)''' tbss_4_prestats, and '''5)''' stats.
to:
As outlined in the TBSS documentation, there are altogether six components to the full analysis: '''0)''' ''Preprocessing'', '''1)''' ''tbss_1_preproc'', '''2)''' ''tbss_2_reg'', '''3)''' ''tbss_3_postreg'', '''4)''' ''tbss_4_prestats'', and '''5)''' ''stats''.
Changed lines 10-11 from:
As outlined in the TBSS documentation, there are altogether six components to the full analysis: 0) '''Preprocessing''', 1) '''tbss_1_preproc''', 2) '''tbss_2_reg''', 3) '''tbss_3_postreg''', 4)'''tbss_4_prestats''', and 5) '''stats'''.
to:
As outlined in the TBSS documentation, there are altogether six components to the full analysis: '''0)''' Preprocessing, '''1)''' tbss_1_preproc, '''2)''' tbss_2_reg, '''3)''' tbss_3_postreg, '''4)''' tbss_4_prestats, and '''5)''' stats.
Changed lines 10-18 from:
As outlined in the TBSS documentation, there are altogether six components to the full analysis:
* '''Preprocessing'''
*
*
*
*
*
to:
As outlined in the TBSS documentation, there are altogether six components to the full analysis: 0) '''Preprocessing''', 1) '''tbss_1_preproc''', 2) '''tbss_2_reg''', 3) '''tbss_3_postreg''', 4)'''tbss_4_prestats''', and 5) '''stats'''.
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!!Custom implementation of tbss_3_postreg
Changed lines 21-24 from:
to:
The integration of DTI-TK output into the TBSS pipeline requires a custom implementation of the fourth step '''tbss_3_postreg'''. The goal is to
* generate the spatially normalized DTI data with a spatial resolution of isotropic 1mm'^3^'.
* generate the mean FA skeleton
Changed lines 19-20 from:
to:
If you have successfully run DTI-TK to spatially normalize of your data into the corresponding group-specific DTI template, you have completed the first '''three''' components in the standard TBSS pipeline.
Changed lines 12-20 from:
* 0: '''Preprocessing'''
* 1: '''tbss_1_preproc'''
* 2: '''tbss_2_reg'''
* 3: '''tbss_3_postreg'''
* 4: '''tbss_4_prestats'''
* 5: '''stats'''
to:
* '''Preprocessing'''
* '''tbss_1_preproc'''
* '''tbss_2_reg'''
* '''tbss_3_postreg'''
* '''tbss_4_prestats'''
* '''stats'''
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* 0: Preprocessing
* 1: tbss_1_preproc
* 2: tbss_2_reg
* 3: tbss_3_postreg
* 4: tbss_4_prestats
* 5: stats
to:
* 0: '''Preprocessing'''
* 1: '''tbss_1_preproc'''
* 2: '''tbss_2_reg'''
* 3: '''tbss_3_postreg'''
* 4: '''tbss_4_prestats'''
* 5: '''stats'''
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!!Overview of the procedures
As outlined in the TBSS documentation, there are altogether six components to the full analysis:
* 0: Preprocessing
* 1: tbss_1_preproc
* 2: tbss_2_reg
* 3: tbss_3_postreg
* 4: tbss_4_prestats
* 5: stats
!!
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This tutorial explains how you can integrate DTI-TK into the standard TBSS pipeline. This affords you the benefit of leveraging the ''state-of-the-art spatial normalization'' provided by DTI-TK together with the ''state-of-the-art voxel-wise statistical inference'' for white matter anatomy. For people who need an explanation of what TBSS is, please refer to [[http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/tbss/index | this FSL page]].
to:
This tutorial explains how you can integrate DTI-TK into the standard TBSS pipeline. This affords you the benefit of leveraging the '''state-of-the-art spatial normalization''' provided by DTI-TK together with the '''state-of-the-art voxel-wise statistical inference''' for white matter anatomy. For people who need an explanation of what TBSS is, please refer to [[http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/tbss/index | this FSL page]].
Changed lines 4-5 from:
This tutorial explains how you can integrate DTI-TK into the standard TBSS pipeline. This affords you the benefit of leveraging the state-of-the-art spatial normalization provided by DTI-TK together with the state-of-the-art voxel-wise statistical inference for white matter anatomy. For people who need an explanation of what TBSS is, please refer to [[http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/tbss/index | this FSL page]].
to:
This tutorial explains how you can integrate DTI-TK into the standard TBSS pipeline. This affords you the benefit of leveraging the ''state-of-the-art spatial normalization'' provided by DTI-TK together with the ''state-of-the-art voxel-wise statistical inference'' for white matter anatomy. For people who need an explanation of what TBSS is, please refer to [[http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/tbss/index | this FSL page]].
Changed lines 4-5 from:
This tutorial how to integrate DTI-TK into the standard TBSS pipeline. If you need an explanation of what TBSS is, refer to [[http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/tbss/index | this FSL page]]. to:
This tutorial explains how you can integrate DTI-TK into the standard TBSS pipeline. This affords you the benefit of leveraging the state-of-the-art spatial normalization provided by DTI-TK together with the state-of-the-art voxel-wise statistical inference for white matter anatomy. For people who need an explanation of what TBSS is, please refer to [[http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/tbss/index | this FSL page]].
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This tutorial how to integrate DTI-TK into the standard TBSS pipeline. If you need an explanation of what TBSS is, refer to [[http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/tbss/index | this FSL page]].
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!Integrate DTI-TK into Tract-Based Spatial Statistics (TBSS)
to:
!Support for Tract-Based Spatial Statistics (TBSS)
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(:noleft:)(:notitle:)(:title DTI-TK support for TBSS:)
!Integrate DTI-TK into Tract-Based Spatial Statistics (TBSS)
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