Camino | Main / Tutorials

May 24, 2013, at 06:54 PM by 165.123.243.100 -

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These tutorials are out of date, please see http://cmic.cs.ucl.ac.uk/camino for current tutorials

to:

These tutorials are out of date, please see http://cmic.cs.ucl.ac.uk/camino for current tutorials and documentation.

While most of the current code is backwards compatible, some of the commands here may no longer work. Please see the current tutorials at the new site before emailing us with problems. Thanks.

May 24, 2013, at 06:49 PM by 165.123.243.100 -

Changed lines 1-2 from:

Here is a list of tutorials to illustrate common operations using Camino:

to:

These tutorials are out of date, please see http://cmic.cs.ucl.ac.uk/camino for current tutorials

May 12, 2011, at 07:37 PM by 64.18.91.187 -

May 12, 2011, at 07:36 PM by 64.18.91.187 -

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More advanced Monte-Carlo Simulations

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More advanced Monte-Carlo Simulations\\

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Other measurement options\\

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Other measurement options

Mapping axon density and diameter with ActiveAx
Example data and data preparation.
Model fitting.
Generating parameter maps.

October 27, 2010, at 11:09 AM by matt -

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October 27, 2010, at 11:09 AM by matt - added link to advanced simulation tutorial

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Explanation of parameters\\

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Explanation of parameters
More advanced Monte-Carlo Simulations This is intended as an overview of the capabilities of the Camino Monte-Carlo simulation. It contains sample commands for different substrates and describes other features of the simualtion that aren't documented elsewhere. Topics covered: Regular-packed cylinder substrates
Disordered, Gamma-distributed cylinder substrates
Crossing fibre substrates
Mesh substrates
Different scheme files
Permeability
Other measurement options\\

June 24, 2010, at 01:59 PM by 128.16.14.149 -

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Connectivity Mapping
Topics covered:

How to construct a connectivity matrix \\

June 24, 2010, at 12:05 PM by 128.16.14.149 -

June 24, 2010, at 11:33 AM by 128.16.14.149 -

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Tractography with q-ball and PASMRI
Topics covered:

Running reduced-encoding PASMRI
Deterministic tractography with PASMRI or q-ball
PICo calibration with PASMRI or q-ball
Probabilistic tractography with PASMRI or q-ball \\

June 21, 2010, at 04:08 PM by 128.16.70.68 -

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More hints

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More hints

Creating a general-waveform schemefile
Topics covered: What is a gen-wave?
Scheme-file format
Explanation of parameters\\

April 27, 2010, at 04:23 PM by cookpa - Adding raw data tutorial

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Input data to Camino
Topics covered:

Conversion of raw data from DICOM to NIfTI
NIfTI conversion to Camino raw format
Dealing with diffusion tensors in NIfTI format

February 25, 2010, at 09:11 AM by Danny -

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Synthetic data from 3D Gaussian functionsSynthetic data using Monte-Carlo simulation\\

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Synthetic data from 3D Gaussian functions
Synthetic data using Monte-Carlo simulation\\

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Constructing data files using shredderSynthetic data for fibre-crossing studies \\

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Constructing data files using shredder
Synthetic data for fibre-crossing studies

October 29, 2009, at 05:10 PM by shahrum -

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October 29, 2009, at 05:10 PM by shahrum -

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http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/cbs/target_meancp.png PICo using waypoints and target ROIs
http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/cbs/cc_labels.png Segmenting brain structures by connectivity \\

to:

http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/cbs/target_meancp.png PICo using waypoints and target ROIs
http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/cbs/cc_labels.png Segmenting brain structures by connectivity \\

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Using camino to produce synthetic data \\

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Using camino to produce synthetic data\\

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Creating masked diffusion tensor imagesUsing flirt to compute affine transformations between images\\

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Creating masked diffusion tensor images
Using flirt to compute affine transformations between images\\

October 29, 2009, at 05:07 PM by shahrum -

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_<Connectivity segmentation: more tractography operations \\

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Connectivity segmentation: more tractography operations \\

October 29, 2009, at 05:07 PM by shahrum -

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Connectivity segmentation: more tractography operations \\

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_<Connectivity segmentation: more tractography operations \\

October 29, 2009, at 05:06 PM by shahrum -

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<-Connectivity segmentation: more tractography operations \\

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Connectivity segmentation: more tractography operations \\

October 29, 2009, at 05:06 PM by shahrum -

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Connectivity segmentation: more tractography operations \\

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<-Connectivity segmentation: more tractography operations \\

October 29, 2009, at 05:05 PM by shahrum -

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http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/miniparallel.png Parallel processing of PICo probability maps. \\

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http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/miniparallel.png Parallel processing of PICo probability maps.\\

October 29, 2009, at 05:04 PM by shahrum -

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October 29, 2009, at 05:03 PM by shahrum -

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Create a Q-Ball ODF map (grey scale and color)Extracting useful information about the peaks of the Q-Ball ODFsVisualising Q-Ball ODF fibre-orientation estimates

to:

Create a Q-Ball ODF map (grey scale and color)
Extracting useful information about the peaks of the Q-Ball ODFs
Visualising Q-Ball ODF fibre-orientation estimates

October 29, 2009, at 05:02 PM by shahrum -

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http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/minipdview.pngViewing the colour-coded direction map with pdview
http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/miniroi.png Using an ROI
http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/minitracks.png Streamline Tractography
http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/minipico.png Probabilistic Tractography using PICo.
http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/miniparallel.png Parallel processing of PICo probability maps. \\

to:

http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/minipdview.pngViewing the colour-coded direction map with pdview
http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/miniroi.png Using an ROI
http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/minitracks.png Streamline Tractography
http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/minipico.png Probabilistic Tractography using PICo.
http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/miniparallel.png Parallel processing of PICo probability maps. \\

October 29, 2009, at 05:01 PM by shahrum -

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http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/PAS_ROI.png

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http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/PAS_ROI.png\\

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http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/mbalign/s32.fmr10_normmi.slice.check.jpg

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http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/mbalign/s32.fmr10_normmi.slice.check.jpg\\

October 29, 2009, at 05:00 PM by shahrum -

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http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/PAS_ROI.png

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http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/PAS_ROI.png Creating PAS plots.

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Creating PAS plots.

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Registering the DWIs within a single acquisition

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Registering the DWIs within a single acquisition
http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/mbalign/s32.fmr10_normmi.slice.check.jpg

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http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/mbalign/s32.fmr10_normmi.slice.check.jpg Preparation before running mbalign\\

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Preparation before running mbalign\\

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More hints\\

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More hints

October 29, 2009, at 04:59 PM by shahrum -

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http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/cbs/cc_labels.png Segmenting brain structures by connectivity

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http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/cbs/cc_labels.png Segmenting brain structures by connectivity

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Topics covered:

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Topics covered:

October 29, 2009, at 04:57 PM by shahrum -

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files/case/minipdview.pngViewing the colour-coded direction map with pdview
files/case/miniroi.png Using an ROI
files/case/minitracks.png Streamline Tractography
files/case/minipico.png Probabilistic Tractography using PICo.
files/case/miniparallel.png Parallel processing of PICo probability maps.

to:

http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/minipdview.pngViewing the colour-coded direction map with pdview
http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/miniroi.png Using an ROI
http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/minitracks.png Streamline Tractography
http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/minipico.png Probabilistic Tractography using PICo.
http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/miniparallel.png Parallel processing of PICo probability maps.

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files/cbs/target_meancp.png PICo using waypoints and target ROIs
files/cbs/cc_labels.png Segmenting brain structures by connectivity

to:

http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/cbs/target_meancp.png PICo using waypoints and target ROIs
http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/cbs/cc_labels.png Segmenting brain structures by connectivity

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files/case/PAS_ROI.pngCreating PAS plots.

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http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/PAS_ROI.png Creating PAS plots.

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Synthetic data from 3D Gaussian functionsSynthetic data using Monte-Carlo simulationGenerating statistics on fibre orientation estimatesConstructing data files using shredderSynthetic data for fibre-crossing studies

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Synthetic data from 3D Gaussian functionsSynthetic data using Monte-Carlo simulation
Generating statistics on fibre orientation estimates
Constructing data files using shredderSynthetic data for fibre-crossing studies

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Creating masked diffusion tensor imagesUsing flirt to compute affine transformations between imagesWarping a diffusion tensor imageReorienting diffusion tensors for consistency with the image transformation

to:

Creating masked diffusion tensor imagesUsing flirt to compute affine transformations between images
Warping a diffusion tensor image
Reorienting diffusion tensors for consistency with the image transformation

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files/mbalign/s32.fmr10_normmi.slice.check.jpg

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http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/mbalign/s32.fmr10_normmi.slice.check.jpg

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Preparation before running mbalign
Run mbalign
Improve performance
Update Gradient5.
More hints

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Preparation before running mbalign
Run mbalign
Improve performance
Update Gradient
More hints\\

October 29, 2009, at 04:54 PM by shahrum -

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files/pig/trd05.png Creating Tr(D) map
files/pig/pds05.png Creating colour-coded direction map
files/pig/favc05.png Detecting fibre crossings

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http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/pig/trd05.png Creating Tr(D) map
http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/pig/pds05.png Creating colour-coded direction map
http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/pig/favc05.png Detecting fibre crossings

October 22, 2009, at 01:15 AM by shahrum -

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http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/pig/fa05.png Creating FA map \\

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http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/pig/fa05.png Creating FA map \\

October 22, 2009, at 01:14 AM by shahrum -

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http://www.cs.ucl.ac.uk/research/medic/camino/files/pig/fa05.png Creating FA map \\

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http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/pig/fa05.png Creating FA map \\

October 22, 2009, at 01:12 AM by shahrum -

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files/pig/fa05.png Creating FA map \\

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http://www.cs.ucl.ac.uk/research/medic/camino/files/pig/fa05.png Creating FA map \\

September 04, 2009, at 04:35 PM by shahrum -

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Using camino to generate and use Q-Ball data ? \\

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Using camino to generate and use Q-Ball data \\

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Tractography tutorial - generating and visualising results ? \\

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Tractography tutorial - generating and visualising results \\

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Connectivity segmentation: more tractography operations ? \\

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Connectivity segmentation: more tractography operations \\

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Running PASMRI using parallel processing ? \\

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Running PASMRI using parallel processing \\

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Using camino to produce synthetic data ? \\

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Using camino to produce synthetic data \\

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Spatial normalization and warping of tensor images ? \\

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Spatial normalization and warping of tensor images \\

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Registering the DWIs within a single acquisition ?

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Registering the DWIs within a single acquisition

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1. Preparation before running mbalign2. Run mbalign3. Improve performance4. Update Gradient5. More hints

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Preparation before running mbalign
Run mbalign
Improve performance
Update Gradient5.
More hints

September 04, 2009, at 04:30 PM by shahrum -

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Detecting Crossing Fibres in the post-mortem pig brain ? \\

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Detecting Crossing Fibres in the post-mortem pig brain \\

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Using camino to generate and use Q-Ball data ? \\

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Using camino to generate and use Q-Ball data ? \\

August 30, 2009, at 11:27 PM by shahrum -

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Detecting Crossing Fibres in the post-mortem pig brain ? \\

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Detecting Crossing Fibres in the post-mortem pig brain ? \\

July 29, 2009, at 03:44 AM by shahrum -

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Here is a list of tutorials to illustrate common operations using Camino:

Detecting Crossing Fibres in the post-mortem pig brain ?
Topics covered:

files/pig/fa05.png Creating FA map
files/pig/trd05.png Creating Tr(D) map
files/pig/pds05.png Creating colour-coded direction map
files/pig/favc05.png Detecting fibre crossings

Using camino to generate and use Q-Ball data ?
Topics covered:

Create a Q-Ball ODF map (grey scale and color)Extracting useful information about the peaks of the Q-Ball ODFsVisualising Q-Ball ODF fibre-orientation estimates

Tractography tutorial - generating and visualising results ?
Topics covered:

files/case/minipdview.pngViewing the colour-coded direction map with pdview
files/case/miniroi.png Using an ROI
files/case/minitracks.png Streamline Tractography
files/case/minipico.png Probabilistic Tractography using PICo.
files/case/miniparallel.png Parallel processing of PICo probability maps.

Connectivity segmentation: more tractography operations ?
Topics covered:

files/cbs/target_meancp.png PICo using waypoints and target ROIs
files/cbs/cc_labels.png Segmenting brain structures by connectivity

Running PASMRI using parallel processing ?
Topics covered:

Running PASMRI using SGE
files/case/PAS_ROI.pngCreating PAS plots.

Using camino to produce synthetic data ?
Topics covered:

Synthetic data from 3D Gaussian functionsSynthetic data using Monte-Carlo simulationGenerating statistics on fibre orientation estimatesConstructing data files using shredderSynthetic data for fibre-crossing studies

Spatial normalization and warping of tensor images ?
Topics covered:

Creating masked diffusion tensor imagesUsing flirt to compute affine transformations between imagesWarping a diffusion tensor imageReorienting diffusion tensors for consistency with the image transformation

Registering the DWIs within a single acquisition ?

files/mbalign/s32.fmr10_normmi.slice.check.jpg

Topics covered:

1. Preparation before running mbalign2. Run mbalign3. Improve performance4. Update Gradient5. More hints

Tutorials

Main.Tutorials History

These tutorials are out of date, please see http://cmic.cs.ucl.ac.uk/camino for current tutorials

These tutorials are out of date, please see http://cmic.cs.ucl.ac.uk/camino for current tutorials and documentation.

While most of the current code is backwards compatible, some of the commands here may no longer work. Please see the current tutorials at the new site before emailing us with problems. Thanks.

These tutorials are out of date, please see http://cmic.cs.ucl.ac.uk/camino for current tutorials