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 These tutorials are out of date, please see [[http://cmic.cs.ucl.ac.uk/camino]] for current tutorials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 These tutorials are out of date, please see [[http://cmic.cs.ucl.ac.uk/camino]] for current tutorials and documentation.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

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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 These tutorials are out of date, please see [[http://cmic.cs.ucl.ac.uk/camino]] for current tutorials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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[[tutorials.advSimTutorial | More advanced Monte-Carlo Simulations]]

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[[tutorials.advSimTutorial | More advanced Monte-Carlo Simulations]]\\

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Other measurement options\\

to:

Other measurement options\\

[[tutorials.ActiveAxTutorial | 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\\

[[tutorials.advSimTutorial | 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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\\

[[tutorials.ConnectivityMapping | 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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\\

[[tutorials.MultiFiberTrack | 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

to:

More hints

[[tutorials.genwaveTutorial | 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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[[tutorials.RawDataTutorial | 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\\

to:

->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
\\

to:

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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->%height=50px% http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/cbs/target_meancp.png PICo using waypoints and target ROIs \\
%height=80px% http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/cbs/cc_labels.png Segmenting brain structures by connectivity \\

to:

->%width=150px% http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/cbs/target_meancp.png PICo using waypoints and target ROIs \\
%width=150px% http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/cbs/cc_labels.png Segmenting brain structures by connectivity \\

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[[tutorials.DataSynthTutorial | Using camino to produce synthetic data]] \\

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[[tutorials.DataSynthTutorial | Using camino to produce synthetic data]]\\

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

to:

->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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_<[[tutorials.ConnectSegmentTutorial | Connectivity segmentation: more tractography operations]] \\

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[[tutorials.ConnectSegmentTutorial | Connectivity segmentation: more tractography operations]] \\

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

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-<[[tutorials.ConnectSegmentTutorial | Connectivity segmentation: more tractography operations]] \\

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_<[[tutorials.ConnectSegmentTutorial | Connectivity segmentation: more tractography operations]] \\

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

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<-[[tutorials.ConnectSegmentTutorial | Connectivity segmentation: more tractography operations]] \\

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-<[[tutorials.ConnectSegmentTutorial | Connectivity segmentation: more tractography operations]] \\

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

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[[tutorials.ConnectSegmentTutorial | Connectivity segmentation: more tractography operations]] \\

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<-[[tutorials.ConnectSegmentTutorial | Connectivity segmentation: more tractography operations]] \\

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

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%width=100px% http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/miniparallel.png Parallel processing of PICo probability maps. \\

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%width=100px% 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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->%height=50px% http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/minipdview.pngViewing the colour-coded direction map with pdview \\
%height=50px% http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/miniroi.png Using an ROI \\
%height=50px% http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/minitracks.png Streamline Tractography \\
%height=50px% http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/minipico.png Probabilistic Tractography using PICo. \\
%height=50px% http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/miniparallel.png Parallel processing of PICo probability maps. \\

to:

->%width=100px% http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/minipdview.pngViewing the colour-coded direction map with pdview \\
%width=100px% http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/miniroi.png Using an ROI \\
%width=100px% http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/minitracks.png Streamline Tractography \\
%width=100px% http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/minipico.png Probabilistic Tractography using PICo. \\
%width=100px% 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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%height=250px% http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/PAS_ROI.png

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%height=250px% http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/PAS_ROI.png\\

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%height=250px% http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/mbalign/s32.fmr10_normmi.slice.check.jpg

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%height=250px% 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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%height=250px% http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/PAS_ROI.png

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%height=50px% 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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[[tutorials.mbalignTutorial | Registering the DWIs within a single acquisition]]

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[[tutorials.mbalignTutorial | Registering the DWIs within a single acquisition]]\\
%height=250px% http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/mbalign/s32.fmr10_normmi.slice.check.jpg

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%height=50px% 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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%height=50px% http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/cbs/cc_labels.png Segmenting brain structures by connectivity \\

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%height=80px% 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:

->%height=50px% http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/minipdview.pngViewing the colour-coded direction map with pdview \\
%height=50px% http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/miniroi.png Using an ROI \\
%height=50px% http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/minitracks.png Streamline Tractography \\
%height=50px% http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/case/minipico.png Probabilistic Tractography using PICo. \\
%height=50px% 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:

->%height=50px% http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/cbs/target_meancp.png PICo using waypoints and target ROIs \\
%height=50px% 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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%height=50px% 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

to:

->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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%height=50px% 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

to:

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

to:

%height=50px% http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/pig/trd05.png Creating Tr(D) map \\
%height=50px% http://www.cs.ucl.ac.uk/research/medic/camino/tutorials/files/pig/pds05.png Creating colour-coded direction map \\
%height=50px% 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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->%height=50px% 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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[[QBallTutorial | Using camino to generate and use Q-Ball data]] \\

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[[tutorials.QBallTutorial | Using camino to generate and use Q-Ball data]] \\

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[[TrackingTutorial.htm | Tractography tutorial - generating and visualising results]] \\

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[[tutorials.TrackingTutorial | Tractography tutorial - generating and visualising results]] \\

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[[ConnectSegmentTutorial.htm | Connectivity segmentation: more tractography operations]] \\

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[[tutorials.ConnectSegmentTutorial | Connectivity segmentation: more tractography operations]] \\

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[[ParallelPAS_Tutorial.htm | Running PASMRI using parallel processing]] \\

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[[tutorials.ParallelPAS_Tutorial | Running PASMRI using parallel processing]] \\

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[[DataSynthTutorial.htm | Using camino to produce synthetic data]] \\

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[[tutorials.DataSynthTutorial | Using camino to produce synthetic data]] \\

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[[SpatialNormTutorial.htm | Spatial normalization and warping of tensor images]] \\

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[[tutorials.SpatialNormTutorial | Spatial normalization and warping of tensor images]] \\

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[[mbalignTutorial.htm | Registering the DWIs within a single acquisition]]

to:

[[tutorials.mbalignTutorial | Registering the DWIs within a single acquisition]]

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

to:

# 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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[[tutorials\PigBrainTutorial.htm | Detecting Crossing Fibres in the post-mortem pig brain]] \\

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[[tutorials.PigBrainTutorial | Detecting Crossing Fibres in the post-mortem pig brain]] \\

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[[QBallTutorial.htm | Using camino to generate and use Q-Ball data]] \\

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[[QBallTutorial | Using camino to generate and use Q-Ball data]] \\

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

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[[PigBrainTutorial.htm | Detecting Crossing Fibres in the post-mortem pig brain]] \\

to:

[[tutorials\PigBrainTutorial.htm | 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:

[[PigBrainTutorial.htm | 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

[[QBallTutorial.htm | 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

[[TrackingTutorial.htm | 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. \\

[[ConnectSegmentTutorial.htm | 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 \\

[[ParallelPAS_Tutorial.htm | Running PASMRI using parallel processing]] \\
Topics covered:

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

[[DataSynthTutorial.htm | 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

[[SpatialNormTutorial.htm | 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

[[mbalignTutorial.htm | 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