Diffusion Processing Pipeline - Revision history

Jadrian Miles: /* Tips */ input restrictions for Q-ball reconstruction on DTK

2014-01-20T01:42:34Z

Tips: input restrictions for Q-ball reconstruction on DTK

← Older revision		Revision as of 01:42, 20 January 2014
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	* Especially when logged in remotely, fork off jobs so that you can log out and keep them running. Remember to use the <tt>notify</tt> target to get an email sent to you once it's done. In <tt>csh</tt>: <pre>make all notify >& make.out &</pre>		* Especially when logged in remotely, fork off jobs so that you can log out and keep them running. Remember to use the <tt>notify</tt> target to get an email sent to you once it's done. In <tt>csh</tt>: <pre>make all notify >& make.out &</pre>
	* DTK is a suite of tools developed by Van Wedeen's group at <abbr title="Massachusetts General Hospital">MGH</abbr> to accomplish the same thing as our processing pipeline: convert input DWIs into a diffusion model, and then perform tractography. DTK implements not only DTI and DTI tractography, but also q-ball and DSI spherical harmonic ODFs and tractography from those. Therefore DTK can be used for comparison in studies where it is appropriate. Trackvis is the streamline viewing program for DTK, analogous to [[Brainapp]]. Both DTK and Trackvis are installed in $G. Note that the DTI fitting algorithm that DTK implements is different than the one we use, and that Trackvis uses its own tractogram file format that is incompatible with Brainapp's.		* DTK is a suite of tools developed by Van Wedeen's group at <abbr title="Massachusetts General Hospital">MGH</abbr> to accomplish the same thing as our processing pipeline: convert input DWIs into a diffusion model, and then perform tractography. DTK implements not only DTI and DTI tractography, but also q-ball and DSI spherical harmonic ODFs and tractography from those. Therefore DTK can be used for comparison in studies where it is appropriate. Trackvis is the streamline viewing program for DTK, analogous to [[Brainapp]]. Both DTK and Trackvis are installed in $G. Note that the DTI fitting algorithm that DTK implements is different than the one we use, and that Trackvis uses its own tractogram file format that is incompatible with Brainapp's.
			** Note that DTK (as of version 0.6.2.2 / 2012.09.20) puts some stupid restrictions on the input format for Q-ball reconstruction:
			*** You must use .nii rather than .nii.gz files. This is because of a bug in the DTK GUI: it strips the .nii.gz extension for the internal representation of the input filename, but then adds a ".nii" when generating the command-line calls to its constituent tools. In this case, the process will fail on the second step (odf_recon). You can either run the command-line tools directly yourself, or use <code>gunzip</code> to fix this.
			*** You must provide a set of sequentially-numbered 3D volumes (not a single 4-D volume with all of them concatenated). If you don't do this, DTK will give you an error complaining about "multiple high b values", even if your gradient table specifies only one. You can use <code>$G/common/mri/niftisplit</code> to get things the way it likes.

	== See Also ==		== See Also ==

Jadrian Miles: /* Tips */

2009-12-03T16:10:33Z

Tips

← Older revision		Revision as of 16:10, 3 December 2009
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	* If you have to do a big batch of datasets, consider [[Run parallel jobs on the Sun Grid Engine\|running them in parallel on the grid engine]].		* If you have to do a big batch of datasets, consider [[Run parallel jobs on the Sun Grid Engine\|running them in parallel on the grid engine]].
	* Especially when logged in remotely, fork off jobs so that you can log out and keep them running. Remember to use the <tt>notify</tt> target to get an email sent to you once it's done. In <tt>csh</tt>: <pre>make all notify >& make.out &</pre>		* Especially when logged in remotely, fork off jobs so that you can log out and keep them running. Remember to use the <tt>notify</tt> target to get an email sent to you once it's done. In <tt>csh</tt>: <pre>make all notify >& make.out &</pre>
	* DTK is a suite of tools developed by Van Wedeen's group at <abbr title="Massachusetts General Hospital">MGH</abbr> to accomplish the same thing as our processing pipeline: convert input DWIs into a diffusion model, and then perform tractography. DTK implements not only DTI and DTI tractography, but also q-ball and DSI spherical harmonic ODFs and tractography from those. Therefore DTK can be used for comparison in studies where it is appropriate. Trackvis is the streamline viewing program for DTK, analogous to [[Brainapp]]. Both DTK and Trackvis are installed in $G.		* DTK is a suite of tools developed by Van Wedeen's group at <abbr title="Massachusetts General Hospital">MGH</abbr> to accomplish the same thing as our processing pipeline: convert input DWIs into a diffusion model, and then perform tractography. DTK implements not only DTI and DTI tractography, but also q-ball and DSI spherical harmonic ODFs and tractography from those. Therefore DTK can be used for comparison in studies where it is appropriate. Trackvis is the streamline viewing program for DTK, analogous to [[Brainapp]]. Both DTK and Trackvis are installed in $G. Note that the DTI fitting algorithm that DTK implements is different than the one we use, and that Trackvis uses its own tractogram file format that is incompatible with Brainapp's.

	== See Also ==		== See Also ==

Jadrian Miles: /* Tips */

2009-12-03T16:09:01Z

Tips

← Older revision		Revision as of 16:09, 3 December 2009
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	== Tips ==		== Tips ==
	* Run jobs on a [[Computing Resources\|fast machine]] rather than your workstation or a CS lab machine.		* Run jobs on a [[Computing Resources\|fast machine]] rather than your workstation or a CS lab machine.
			* If you have to do a big batch of datasets, consider [[Run parallel jobs on the Sun Grid Engine\|running them in parallel on the grid engine]].
	* Especially when logged in remotely, fork off jobs so that you can log out and keep them running. Remember to use the <tt>notify</tt> target to get an email sent to you once it's done. In <tt>csh</tt>: <pre>make all notify >& make.out &</pre>		* Especially when logged in remotely, fork off jobs so that you can log out and keep them running. Remember to use the <tt>notify</tt> target to get an email sent to you once it's done. In <tt>csh</tt>: <pre>make all notify >& make.out &</pre>
	* DTK is a suite of tools developed by Van Wedeen's group at <abbr title="Massachusetts General Hospital">MGH</abbr> to accomplish the same thing as our processing pipeline: convert input DWIs into a diffusion model, and then perform tractography. DTK implements not only DTI and DTI tractography, but also q-ball and DSI spherical harmonic ODFs and tractography from those. Therefore DTK can be used for comparison in studies where it is appropriate. Trackvis is the streamline viewing program for DTK, analogous to [[Brainapp]]. Both DTK and Trackvis are installed in $G.		* DTK is a suite of tools developed by Van Wedeen's group at <abbr title="Massachusetts General Hospital">MGH</abbr> to accomplish the same thing as our processing pipeline: convert input DWIs into a diffusion model, and then perform tractography. DTK implements not only DTI and DTI tractography, but also q-ball and DSI spherical harmonic ODFs and tractography from those. Therefore DTK can be used for comparison in studies where it is appropriate. Trackvis is the streamline viewing program for DTK, analogous to [[Brainapp]]. Both DTK and Trackvis are installed in $G.

Jadrian Miles: /* Tips */

2009-11-06T01:00:17Z

Tips

← Older revision		Revision as of 01:00, 6 November 2009
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	* Run jobs on a [[Computing Resources\|fast machine]] rather than your workstation or a CS lab machine.		* Run jobs on a [[Computing Resources\|fast machine]] rather than your workstation or a CS lab machine.
	* Especially when logged in remotely, fork off jobs so that you can log out and keep them running. Remember to use the <tt>notify</tt> target to get an email sent to you once it's done. In <tt>csh</tt>: <pre>make all notify >& make.out &</pre>		* Especially when logged in remotely, fork off jobs so that you can log out and keep them running. Remember to use the <tt>notify</tt> target to get an email sent to you once it's done. In <tt>csh</tt>: <pre>make all notify >& make.out &</pre>
	* DTK is a suite of tools developed at <abbr title="Massachusetts General Hospital">MGH</abbr> to accomplish the same thing as our processing pipeline: convert input DWIs into a diffusion model, and then perform tractography. DTK implements not only DTI and DTI tractography, but also q-ball and DSI spherical harmonic ODFs and tractography from those. Therefore DTK can be used for comparison in studies where it is appropriate. Trackvis is the streamline viewing program for DTK, analogous to [[Brainapp]]. Both DTK and Trackvis are installed in $G.		* DTK is a suite of tools developed by Van Wedeen's group at <abbr title="Massachusetts General Hospital">MGH</abbr> to accomplish the same thing as our processing pipeline: convert input DWIs into a diffusion model, and then perform tractography. DTK implements not only DTI and DTI tractography, but also q-ball and DSI spherical harmonic ODFs and tractography from those. Therefore DTK can be used for comparison in studies where it is appropriate. Trackvis is the streamline viewing program for DTK, analogous to [[Brainapp]]. Both DTK and Trackvis are installed in $G.

	== See Also ==		== See Also ==

Jadrian Miles: /* Tips */

2009-11-06T00:59:50Z

Tips

← Older revision		Revision as of 00:59, 6 November 2009
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	* Run jobs on a [[Computing Resources\|fast machine]] rather than your workstation or a CS lab machine.		* Run jobs on a [[Computing Resources\|fast machine]] rather than your workstation or a CS lab machine.
	* Especially when logged in remotely, fork off jobs so that you can log out and keep them running. Remember to use the <tt>notify</tt> target to get an email sent to you once it's done. In <tt>csh</tt>: <pre>make all notify >& make.out &</pre>		* Especially when logged in remotely, fork off jobs so that you can log out and keep them running. Remember to use the <tt>notify</tt> target to get an email sent to you once it's done. In <tt>csh</tt>: <pre>make all notify >& make.out &</pre>
	* DTK is a suite of tools developed at <abbr title="Massachusetts General Hospital">MGH</a> to accomplish the same thing as our processing pipeline: convert input DWIs into a diffusion model, and then perform tractography. DTK implements not only DTI and DTI tractography, but also q-ball and DSI spherical harmonic ODFs and tractography from those. Therefore DTK can be used for comparison in studies where it is appropriate. Trackvis is the streamline viewing program for DTK, analogous to [[Brainapp]]. Both DTK and Trackvis are installed in $G.		* DTK is a suite of tools developed at <abbr title="Massachusetts General Hospital">MGH</abbr> to accomplish the same thing as our processing pipeline: convert input DWIs into a diffusion model, and then perform tractography. DTK implements not only DTI and DTI tractography, but also q-ball and DSI spherical harmonic ODFs and tractography from those. Therefore DTK can be used for comparison in studies where it is appropriate. Trackvis is the streamline viewing program for DTK, analogous to [[Brainapp]]. Both DTK and Trackvis are installed in $G.

	== See Also ==		== See Also ==

Jadrian Miles: /* Tips */

2009-11-06T00:59:40Z

Tips

← Older revision		Revision as of 00:59, 6 November 2009
Line 56:		Line 56:
	* Run jobs on a [[Computing Resources\|fast machine]] rather than your workstation or a CS lab machine.		* Run jobs on a [[Computing Resources\|fast machine]] rather than your workstation or a CS lab machine.
	* Especially when logged in remotely, fork off jobs so that you can log out and keep them running. Remember to use the <tt>notify</tt> target to get an email sent to you once it's done. In <tt>csh</tt>: <pre>make all notify >& make.out &</pre>		* Especially when logged in remotely, fork off jobs so that you can log out and keep them running. Remember to use the <tt>notify</tt> target to get an email sent to you once it's done. In <tt>csh</tt>: <pre>make all notify >& make.out &</pre>
			* DTK is a suite of tools developed at <abbr title="Massachusetts General Hospital">MGH</a> to accomplish the same thing as our processing pipeline: convert input DWIs into a diffusion model, and then perform tractography. DTK implements not only DTI and DTI tractography, but also q-ball and DSI spherical harmonic ODFs and tractography from those. Therefore DTK can be used for comparison in studies where it is appropriate. Trackvis is the streamline viewing program for DTK, analogous to [[Brainapp]]. Both DTK and Trackvis are installed in $G.

	== See Also ==		== See Also ==

Jadrian Miles: /* See Also */

2009-03-22T21:30:20Z

Jadrian Miles: /* Step 2: Process DWIs */

2009-03-18T15:47:04Z

Step 2: Process DWIs

← Older revision		Revision as of 15:47, 18 March 2009
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	* <code>$G/bin/mrifilt3</code> --- resample images to match a specified voxel volume		* <code>$G/bin/mrifilt3</code> --- resample images to match a specified voxel volume
	* <code>$dbin/diffusionResize.py</code> --- by calling the previous two, automatically resample, crop, and pad images to a specified spatial volume in mm, sampled by a specified voxel volume		* <code>$dbin/diffusionResize.py</code> --- by calling the previous two, automatically resample, crop, and pad images to a specified spatial volume in mm, sampled by a specified voxel volume
			* <code>$G/bin/mritransp</code> --- permute and/or flip dimensions in a DWI

	=== Step 3: Generate (and Possibly Process) Tensors ===		=== Step 3: Generate (and Possibly Process) Tensors ===

Jadrian Miles at 15:24, 18 March 2009

2009-03-18T15:24:17Z

← Older revision		Revision as of 15:24, 18 March 2009
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	Right now little of the code used in the processing pipeline is checked into [[$G]], and those programs that are checked in are usually very small and scattered around the source tree. After Brad's new system is in place, he and Jadrian will work on getting all the scripts we use fixed up and checked into a single location. In the text below, the prefix <code>$dbin</code> means <code>/map/gfx0/common0/diffusion/Interface/bin/data</code>, where a lot of scripts currently live.		Right now little of the code used in the processing pipeline is checked into [[$G]], and those programs that are checked in are usually very small and scattered around the source tree. After Brad's new system is in place, he and Jadrian will work on getting all the scripts we use fixed up and checked into a single location. In the text below, the prefix <code>$dbin</code> means <code>/map/gfx0/common0/diffusion/Interface/bin/data</code>, where a lot of scripts currently live.

			{{warning\|'''Note:''' if you're running the pipeline for the first time on data from a new protocol, you'll probably discover [[Diagnose tensor orientation problems\|orientation problems]] or other issues. It's a real drag to wait around for long processes to complete just to discover that the output is bad. Do yourself a favor and '''do a test run [[Run the diffusion processing pipeline at low resolution\|at low resolution]]!'''}}

	== Pipeline Steps ==		== Pipeline Steps ==

Jadrian Miles: /* Step 4: Generate Tensor Metrics */

2009-03-13T14:07:08Z

Step 4: Generate Tensor Metrics

← Older revision		Revision as of 14:07, 13 March 2009
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	We can generate a plethora of scalar metrics from tensors, including FA, trace, and similar things.		We can generate a plethora of scalar metrics from tensors, including FA, trace, and similar things.

	* <code>$G/bin/mritensor_v0</code> --- has a huge menu of options; give it the <code>--</code> argument to see a list		* <code>$G/bin/mritensor_v0</code> --- has a huge menu of options; give it the <code><nowiki>--</nowiki></code> argument to see a list

	=== Step 5: Generate Streamtubes ===		=== Step 5: Generate Streamtubes ===

← Older revision		Revision as of 21:30, 22 March 2009
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	== See Also ==		== See Also ==
	* [[Diffusion Processing Pipeline/bugs and feature requests\|Pipeline bugs and feature requests]]		* [[Diffusion Processing Pipeline/bugs and feature requests\|Pipeline bugs and feature requests]]
			* [[In-House Diffusion MRI Software]]

	[[Category:Diffusion MRI]][[Category:Software]]		[[Category:Diffusion MRI]][[Category:Software]]