Diffusion MRI Design Notes - Revision history

Nathan Malkin: pipeline sketch

2010-08-17T22:11:23Z

pipeline sketch

← Older revision		Revision as of 22:11, 17 August 2010
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	* Win's Pipeline - In project/brain/pipeline/coro/ and install_linux/bin/brain/		[[Image:Pipelines.jpg\|1000px]]

			* <span style="color:blue">Win's Pipeline</span> - In project/brain/pipeline/coro/ and install_linux/bin/brain/

	coro_dicom2nifti.py - Dicom files ==> Nifti		coro_dicom2nifti.py - Dicom files ==> Nifti
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	* Legacy Pipeline - In project/brain/pipeline/ and install_linux/bin/brain/		* <span style="color:green">Legacy Pipeline</span> - In project/brain/pipeline/ and install_linux/bin/brain/

	format_conversion/ nifti2mriimage - Registered nifti DWI ==> MRI Image		format_conversion/ nifti2mriimage - Registered nifti DWI ==> MRI Image
	tensor/mritensorop/ mritensor - Mri Image ==> DTI and scalar images		tensor/mritensorop/ mritensor - Mri Image ==> DTI and scalar images
	streamtube/tubegen/ tubegen - DTI ==> DTI tractogram		streamtube/tubegen/ tubegen - DTI ==> DTI tractogram

	tubefa???		tubefa???
	project/brain/brainapp - Interactively create statistics.		project/brain/brainapp - Interactively create statistics.


	* DTK Pipeline tools - In import/dtk/dtk_v0.5_linux/ and import/dtk/trackvis_v0.5_linux/		* <span style="color:purple">DTK Pipeline tools</span> - In import/dtk/dtk_v0.5_linux/ and import/dtk/trackvis_v0.5_linux/

	DTK - DWI => DTI or QBI		DTK - DWI => DTI or QBI

Brad Berg at 19:53, 16 August 2010

2010-08-16T19:53:03Z

← Older revision		Revision as of 19:53, 16 August 2010
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	* Win's Pipeline - In project/brain/pipeline/coro/ and install_linux/bin/brain/		* Win's Pipeline - In project/brain/pipeline/coro/ and install_linux/bin/brain/

	coro_dicom2nifti.py - Dicom files ==> Nifti		coro_dicom2nifti.py - Dicom files ==> Nifti
	coro_register.py - Coregister a set of MRI images against a reference template image.		coro_register.py - Coregister a set of MRI images against a reference template image.
	Produce registered nifti DWIs for performing dti steps.		Produce registered nifti DWIs for performing dti steps.

Jadrian Miles: Corrected spellings of "nifti"

2010-08-16T19:23:16Z

Corrected spellings of "nifti"

← Older revision		Revision as of 19:23, 16 August 2010
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	* Win's Pipeline - In project/brain/pipeline/coro/ and install_linux/bin/brain/		* Win's Pipeline - In project/brain/pipeline/coro/ and install_linux/bin/brain/

	~~coro_dicom2niifti~~.py - Dicom files ==> ~~Niifti~~		coro_dicom2nifti.py - Dicom files ==> Nifti
	coro_register.py - Coregister a set of MRI images against a reference template image.		coro_register.py - Coregister a set of MRI images against a reference template image.
	Produce registered ~~niifti~~ DWIs for performing dti steps.		Produce registered nifti DWIs for performing dti steps.
	Also creates registration matricies.		Also creates registration matricies.
	coro_dti.py - Compute a dti; the CIT pipeline does a better job.		coro_dti.py - Compute a dti; the CIT pipeline does a better job.
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	* Legacy Pipeline - In project/brain/pipeline/ and install_linux/bin/brain/		* Legacy Pipeline - In project/brain/pipeline/ and install_linux/bin/brain/

	format_conversion/ ~~niftii2mriimage~~ - Registered ~~niifti~~ DWI ==> MRI Image		format_conversion/ nifti2mriimage - Registered nifti DWI ==> MRI Image
	tensor/mritensorop/ mritensor - Mri Image ==> DTI and scalar images		tensor/mritensorop/ mritensor - Mri Image ==> DTI and scalar images
	streamtube/tubegen/ tubegen - DTI ==> DTI tractogram		streamtube/tubegen/ tubegen - DTI ==> DTI tractogram

Brad Berg at 19:19, 16 August 2010

2010-08-16T19:19:45Z

← Older revision		Revision as of 19:19, 16 August 2010
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	coro_register.py - Coregister a set of MRI images against a reference template image.		coro_register.py - Coregister a set of MRI images against a reference template image.
	Produce registered niifti DWIs for performing dti steps.		Produce registered niifti DWIs for performing dti steps.
			Also creates registration matricies.
	coro_dti.py - Compute a dti; the CIT pipeline does a better job.		coro_dti.py - Compute a dti; the CIT pipeline does a better job.

Brad Berg at 19:18, 16 August 2010

2010-08-16T19:18:21Z

← Older revision		Revision as of 19:18, 16 August 2010
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	NYI: Simple Tubegen - DTI and scalar images ==> Tracts		NYI: Simple Tubegen - DTI and scalar images ==> Tracts
	Scalar sampling		Scalar sampling
	Tractogram culling		common/libcurvecollection/ -Tractogram culling
	Boolean ROI selection		Boolean ROI selection
	Stats		Stats
	project/brain/roi_select/ - Tract filtering.		project/brain/roi_select/ - Tract filtering.


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	==> Run the script ==> Intermediate and result files.		==> Run the script ==> Intermediate and result files.
	==> Log output		==> Log output
			common/libcurvecollection

Brad Berg at 19:11, 16 August 2010

2010-08-16T19:11:03Z

← Older revision		Revision as of 19:11, 16 August 2010
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	* GUI Pipeline Interface		* GUI Pipeline Interface

	Configuration file (.cfg) + Data ==> Custom Python Script (or Makefile or Sh script)		Configuration file (.cfg) + Data ==> Custom Python Script (or Makefile or Sh script)
	==> Run the script ==> Intermediate and result files.		==> Run the script ==> Intermediate and result files.
	==> Log output		==> Log output

Brad Berg at 19:10, 16 August 2010

2010-08-16T19:10:23Z

← Older revision		Revision as of 19:10, 16 August 2010
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	* Win's Pipeline - In project/brain/pipeline/coro/ and install_linux/bin/brain/		* Win's Pipeline - In project/brain/pipeline/coro/ and install_linux/bin/brain/

	coro_dicom2niifti.py - ~~Convert~~ Dicom files to Niifti ~~format.~~		coro_dicom2niifti.py - Dicom files ==> Niifti
	coro_register.py - Coregister a set of MRI images against a reference template image.		coro_register.py - Coregister a set of MRI images against a reference template image.
	Produce registered niifti DWIs for performing dti steps.		Produce registered niifti DWIs for performing dti steps.
	coro_dti.py - Compute a dti; the CIT ~~pipelne~~ does a better job.		coro_dti.py - Compute a dti; the CIT pipeline does a better job.


	* Legacy Pipeline - In project/brain/pipeline/ and install_linux/bin/brain/		* Legacy Pipeline - In project/brain/pipeline/ and install_linux/bin/brain/

	format_conversion/ niftii2mriimage - ~~Convert a registered~~ niifti DWI ~~to Mri~~ Image ~~format.~~		format_conversion/ niftii2mriimage - Registered niifti DWI ==> MRI Image
	tensor/mritensorop/ mritensor - ~~Convert an~~ Mri Image ~~to a~~ DTI and scalar images.		tensor/mritensorop/ mritensor - Mri Image ==> DTI and scalar images
	streamtube/tubegen/ tubegen - ~~Convert a~~ DTI ~~to a~~ DTI tractogram.		streamtube/tubegen/ tubegen - DTI ==> DTI tractogram

	tubefa???		tubefa???
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	* DTK Pipeline tools - In import/dtk/dtk_v0.5_linux/ and import/dtk/trackvis_v0.5_linux/		* DTK Pipeline tools - In import/dtk/dtk_v0.5_linux/ and import/dtk/trackvis_v0.5_linux/

	DTK - ~~Convert DWIs to either a~~ DTI or QBI.		DTK - DWI => DTI or QBI
	The CIT pipeline does a better job.		The CIT pipeline does a better job.
	DTK - ~~Convert a~~ DTI or QBI to a tractogram		DTK - DTI or QBI ==> a tractogram
	TrackVis - ~~Convert~~ a tractogram or QBI ~~to statistics~~.		TrackVis - Produce statistics from a tractogram or QBI.


	* New Pipeline in the Works		* New Pipeline in the Works

			NYI: Simple Tubegen - DTI and scalar images ==> Tracts
			Scalar sampling
			Tractogram culling
			Boolean ROI selection
			Stats
			project/brain/roi_select/ - Tract filtering.


			* GUI Pipeline Interface

			Configuration file (.cfg) + Data ==> Custom Python Script (or Makefile or Sh script)
			==> Run the script ==> Intermediate and result files.
			==> Log output

Brad Berg: New page: This page is a work in progress. * Win's Pipeline - In project/brain/pipeline/coro/ and install_linux/bin/brain/ coro_dicom2niifti.py - Convert Dicom files to Niifti format. coro_regi...

2010-08-16T18:35:56Z

New page: This page is a work in progress. * Win's Pipeline - In project/brain/pipeline/coro/ and install_linux/bin/brain/ coro_dicom2niifti.py - Convert Dicom files to Niifti format. coro_regi...

New page

This page is a work in progress.

* Win's Pipeline - In project/brain/pipeline/coro/ and install_linux/bin/brain/

coro_dicom2niifti.py - Convert Dicom files to Niifti format.
coro_register.py - Coregister a set of MRI images against a reference template image.
Produce registered niifti DWIs for performing dti steps.
coro_dti.py - Compute a dti; the CIT pipelne does a better job.

* Legacy Pipeline - In project/brain/pipeline/ and install_linux/bin/brain/

format_conversion/ niftii2mriimage - Convert a registered niifti DWI to Mri Image format.
tensor/mritensorop/ mritensor - Convert an Mri Image to a DTI and scalar images.
streamtube/tubegen/ tubegen - Convert a DTI to a DTI tractogram.

tubefa???
project/brain/brainapp - Interactively create statistics.

* DTK Pipeline tools - In import/dtk/dtk_v0.5_linux/ and import/dtk/trackvis_v0.5_linux/

DTK - Convert DWIs to either a DTI or QBI.
The CIT pipeline does a better job.
DTK - Convert a DTI or QBI to a tractogram
TrackVis - Convert a tractogram or QBI to statistics.

* New Pipeline in the Works