ADC map registration

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

ADC map registration

Felix
Dear Slicer users,

I'm using Brainsfit to register ADC maps. I scanned 5 times to the same
volunteer in order to obtain the repatability of these maps.

Even using immobilizer small movements and rotations appear so I need to
register all the images. Since the slice thickness is 5 mm for those ADC
maps I suppose that I cannot expect very good results from the registering
process.

A T1 weighted image with 1 mm3  per voxel was scanned in the same session
(to be used for freesurfer) so I tried to use it as fixed image in my second
attempt instead of the first ADC map.

I used rigid rotations but the results that I obtained seemed like needing
an additional BSpline non rigid registration. I used MSE for the first
attemp and MMI for the second one with the structural image as fixed one.

Since the results do no seem to be as good as I expected, do any of you have
experience enough to tell me if these parameters are correct?

                 '--maskProcessingMode ROI',
                 '--fixedBinaryVolume mask.nii.gz --movingBinaryVolume
mask.nii.gz',
                 '--useRigid --use BSpline',              
                 '--samplingPercentage 0.05 --initializeTransformMode Off',
                 '--splineGridSize 4,4,4 --maxBSplineDisplacement 10',
                 '--medianFilterSize 0,0,0 --removeIntensityOutliers 0
--outputVolumePixelType int',
                 '--backgroundFillValue 0 --interpolationMode WindowedSinc',
                 '--numberOfIterations 1500 --maximumStepLength 0.5
--minimumStepLength 0.001',
                 '--relaxationFactor 0.5 --translationScale 1000',
                 ' --reproportionScale 1 --skewScale 1',
                 '--numberOfHistogramBins 50 --numberOfMatchPoints 10',
                 '--costMetric MMI',  #MSE for ADC/ADC
                 '--ROIAutoDilateSize 0 --ROIAutoClosingSize 9',
                 '--costFunctionConvergenceFactor 1000
--projectedGradientTolerance 0.0001',
                 '--maximumNumberOfEvaluations 900
--maximumNumberOfCorrections 25',
                 '--metricSamplingStrategy Random',
                 '--fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0',
                 '--maskInferiorCutOffFromCenter 1000  --numberOfSamples 0
--failureExitCode -1 --numberOfThreads -1',
                 '--debugLevel 0 --echo'

Rigid registration finished after 35-40 iterations and non-rigid
registration used around 25 iterations.

Do any of you have any suggestion about these parameters?

Thank you in advance.

Félix.



--
View this message in context: http://slicer-users.65878.n3.nabble.com/ADC-map-registration-tp4032173.html
Sent from the slicer-users mailing list archive at Nabble.com.
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
Reply | Threaded
Open this post in threaded view
|

Re: ADC map registration

inorton
Hi Felix,

I re-posted and replied with some comments on Discourse:


Best,
Isaiah

On Mon, Apr 10, 2017 at 6:07 PM, Felix <[hidden email]> wrote:
Dear Slicer users,

I'm using Brainsfit to register ADC maps. I scanned 5 times to the same
volunteer in order to obtain the repatability of these maps.

Even using immobilizer small movements and rotations appear so I need to
register all the images. Since the slice thickness is 5 mm for those ADC
maps I suppose that I cannot expect very good results from the registering
process.

A T1 weighted image with 1 mm3  per voxel was scanned in the same session
(to be used for freesurfer) so I tried to use it as fixed image in my second
attempt instead of the first ADC map.

I used rigid rotations but the results that I obtained seemed like needing
an additional BSpline non rigid registration. I used MSE for the first
attemp and MMI for the second one with the structural image as fixed one.

Since the results do no seem to be as good as I expected, do any of you have
experience enough to tell me if these parameters are correct?

                 '--maskProcessingMode ROI',
                 '--fixedBinaryVolume mask.nii.gz --movingBinaryVolume
mask.nii.gz',
                 '--useRigid --use BSpline',
                 '--samplingPercentage 0.05 --initializeTransformMode Off',
                 '--splineGridSize 4,4,4 --maxBSplineDisplacement 10',
                 '--medianFilterSize 0,0,0 --removeIntensityOutliers 0
--outputVolumePixelType int',
                 '--backgroundFillValue 0 --interpolationMode WindowedSinc',
                 '--numberOfIterations 1500 --maximumStepLength 0.5
--minimumStepLength 0.001',
                 '--relaxationFactor 0.5 --translationScale 1000',
                 ' --reproportionScale 1 --skewScale 1',
                 '--numberOfHistogramBins 50 --numberOfMatchPoints 10',
                 '--costMetric MMI',  #MSE for ADC/ADC
                 '--ROIAutoDilateSize 0 --ROIAutoClosingSize 9',
                 '--costFunctionConvergenceFactor 1000
--projectedGradientTolerance 0.0001',
                 '--maximumNumberOfEvaluations 900
--maximumNumberOfCorrections 25',
                 '--metricSamplingStrategy Random',
                 '--fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0',
                 '--maskInferiorCutOffFromCenter 1000  --numberOfSamples 0
--failureExitCode -1 --numberOfThreads -1',
                 '--debugLevel 0 --echo'

Rigid registration finished after 35-40 iterations and non-rigid
registration used around 25 iterations.

Do any of you have any suggestion about these parameters?

Thank you in advance.

Félix.



--
View this message in context: http://slicer-users.65878.n3.nabble.com/ADC-map-registration-tp4032173.html
Sent from the slicer-users mailing list archive at Nabble.com.
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ