Whole Brain Tractography

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Whole Brain Tractography

Peter Neher
Hi all,

I just wanted to check out the new whole brain tractography feature of
slicer 4 but the according module does not seem to contain any
functionality. Is this module still work in progress?

Best regards
Peter
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Re: Whole Brain Tractography

Kikinis, Ron,M.D.
Did you try the nightly build? What platform?

On 5/29/12 9:08 AM, Peter Neher wrote:

> Hi all,
>
> I just wanted to check out the new whole brain tractography feature of
> slicer 4 but the according module does not seem to contain any
> functionality. Is this module still work in progress?
>
> Best regards
> Peter
> _______________________________________________
> 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

--
Ron Kikinis, M.D.,
Robert Greenes Distinguished Director of Biomedical Informatics
Professor of Radiology, Harvard Medical School
Director, Surgical Planning Laboratory
http://www.spl.harvard.edu/~kikinis
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Re: Whole Brain Tractography

Peter Neher
I am using the precompiled 4.1. binaries under Ubuntu 12.4 (64 bit).
Screenshot of the application attached. I also tried it with a diffusion
weighted dataset loaded, but that didn't change anything.

On 05/29/2012 03:14 PM, Ron Kikinis wrote:

> Did you try the nightly build? What platform?
>
> On 5/29/12 9:08 AM, Peter Neher wrote:
>> Hi all,
>>
>> I just wanted to check out the new whole brain tractography feature of
>> slicer 4 but the according module does not seem to contain any
>> functionality. Is this module still work in progress?
>>
>> Best regards
>> Peter
>> _______________________________________________
>> 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

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Re: Whole Brain Tractography

Julien Finet
Can you send the logs in the dialog that popups by doing Ctrl+0 ?
Thanks,
j.

On Tue, May 29, 2012 at 9:22 AM, Peter Neher <[hidden email]> wrote:
I am using the precompiled 4.1. binaries under Ubuntu 12.4 (64 bit). Screenshot of the application attached. I also tried it with a diffusion weighted dataset loaded, but that didn't change anything.


On 05/29/2012 03:14 PM, Ron Kikinis wrote:
Did you try the nightly build? What platform?

On 5/29/12 9:08 AM, Peter Neher wrote:
Hi all,

I just wanted to check out the new whole brain tractography feature of
slicer 4 but the according module does not seem to contain any
functionality. Is this module still work in progress?

Best regards
Peter
_______________________________________________
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

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Re: Whole Brain Tractography

Demian Wassermann-2
In reply to this post by Peter Neher
Hello Peter,

While we figure out what is wrong with the binary distribution, you replicate the wizard by hand:

You can obtain the diffusion tensor image from your DICOM following the "SLICER4 DIFFUSION TENSOR IMAGING TUTORIAL" at

http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Training

Then if you use the labelmap seeding module without any mask, you will obtain a full brain tractography

HTH
Demian

--
Demian Wassermann, PhD
[hidden email]
LMI / PNL / SPL Labs
Harvard Medical School
Brigham and Women's Hospital
1249 Boylston, Boston, MA, USA
http://lmi.bwh.harvard.edu/~wassermann/

On May 29, 2012, at 9:08 AM, Peter Neher wrote:

> Hi all,
>
> I just wanted to check out the new whole brain tractography feature of
> slicer 4 but the according module does not seem to contain any
> functionality. Is this module still work in progress?
>
> Best regards
> Peter
> _______________________________________________
> 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

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Re: Whole Brain Tractography

Peter Neher
In reply to this post by Julien Finet
Is there a way to export the log as .txt? Anyways, here are the messages:

Debugt Qt:

Number of registered modules: 98

Register compression libraries


Debug Qt:

Number of instantiated modules: 98


Critical FD: nothing here


Info FD: nothing here


Debug Qt:

Loading module "ACPCTransform"

Loading module "AddScalarVolumes"

Loading module "AffineRegistration"

Loading module "Annotations"

RegisterIO "qSlicerAnnotationsIO"

RegisterIO "qSlicerFiducialsIO"

Loading module "BRAINSDemonWarp"

Loading module "BRAINSFit"

Loading module "BRAINSROIAuto"

Loading module "BRAINSResample"

Loading module "BSplineDeformableRegistration"

Loading module "BSplineToDeformationField"

Loading module "Cameras"

Loading module "CastScalarVolume"

Loading module "ChangeTracker"

Loading module "CheckerBoardFilter"

Loading module "Colors"

RegisterIO "qSlicerColorsIO"

Loading module "CreateDICOMSeries"

Loading module "CropVolume"

RegisterIO "qSlicerVolumesIO"

Loading module "CurvatureAnisotropicDiffusion"

Loading module "DICOM"

Loading module "DICOM2FullBrainTractography"

Loading module "DICOMDiffusionVolumePlugin"

Loading module "DICOMScalarVolumePlugin"

Loading module "DICOMSlicerDataBundlePlugin"

Loading module "DTIexport"

Loading module "DTIimport"

Loading module "DWIJointRicianLMMSEFilter"

Loading module "DWIRicianLMMSEFilter"

Loading module "DWIToDTIEstimation"

Loading module "DWIUnbiasedNonLocalMeansFilter"

Loading module "Data"

RegisterIO "qSlicerSceneIO"

RegisterIO "qSlicerSlicer2SceneReader"

RegisterIO "qSlicerXcedeCatalogIO"

Loading module "DataProbe"

Loading module "DicomToNrrdConverter"

Loading module "DiffusionTensorScalarMeasurements"

Loading module "DiffusionWeightedVolumeMasking"

Loading module "EMSegment"

Loading module "EMSegmentCommandLine"

Loading module "EMSegmentQuick"

Loading module "EMSegmentTransformToNewFormat"

Loading module "Editor"

Loading module "Endoscopy"

Loading module "EventBroker"

Loading module "ExecutionModelTour"

Loading module "ExpertAutomatedRegistration"

Loading module "ExtractSkeleton"

Loading module "FiducialRegistration"

Loading module "GaussianBlurImageFilter"

Loading module "GradientAnisotropicDiffusion"

Loading module "GrayscaleFillHoleImageFilter"

Loading module "GrayscaleGrindPeakImageFilter"

Loading module "GrayscaleModelMaker"

Loading module "HistogramMatching"

Loading module "ImageLabelCombine"

Loading module "IntensityDifferenceMetric"

Loading module "LabelMapSmoothing"

Loading module "LabelStatistics"

Loading module "LinearRegistration"

Loading module "MaskScalarVolume"

Loading module "MedianImageFilter"

Loading module "MergeModels"

Loading module "ModelMaker"

Loading module "ModelToLabelMap"

Loading module "Models"

RegisterIO "qSlicerModelsIO"

RegisterIO "qSlicerScalarOverlayIO"

Loading module "ModuleTemplate"

Loading module "MultiResolutionAffineRegistration"

Loading module "MultiVolumeExplorer"

Loading module "MultiVolumeImporter"

Loading module "MultiplyScalarVolumes"

Loading module "N4ITKBiasFieldCorrection"

Loading module "OpenIGTLinkIF"

Loading module "OrientScalarVolume"

Loading module "OtsuThresholdImageFilter"

Loading module "OtsuThresholdSegmentation"

Loading module "PETStandardUptakeValueComputation"

Loading module "PerformanceTests"

Loading module "ProbeVolumeWithModel"

Loading module "Reformat"

Loading module "ResampleDTIVolume"

Loading module "ResampleScalarVectorDWIVolume"

Loading module "ResampleScalarVolume"

Loading module "RigidRegistration"

Loading module "RobustStatisticsSegmenter"

Loading module "SampleData"

Loading module "SceneViews"

Loading module "SimpleRegionGrowingSegmentation"

Loading module "SubtractScalarVolumes"

Loading module "ThresholdScalarVolume"

Loading module "Tractography"

Loading module "TractographyDisplay"

RegisterIO "qSlicerFiberBundleIO"

Loading module "TractographyFiducialSeeding"

Loading module "TractographyLabelMapSeeding"

Loading module "Transforms"

RegisterIO "qSlicerTransformsIO"

Loading module "VBRAINSDemonWarp"

Loading module "ViewControllers"

Loading module "VolumeRendering"

RegisterIO "qSlicerVolumeRenderingIO"

Loading module "Volumes"

Loading module "VotingBinaryHoleFillingImageFilter"

Loading module "WebGLExport"

Loading module "Welcome"

Number of loaded modules: 98

Show module (name): "Welcome"


Debug Qt:

Show module (name): "DICOM2FullBrainTractography"


Debug Qt:

onEntryInternal - entering input from

processingAfterOnEntry

showUserInterface - showing


Peter

On 05/29/2012 10:17 PM, Julien Finet wrote:
Can you send the logs in the dialog that popups by doing Ctrl+0 ?
Thanks,
j.

On Tue, May 29, 2012 at 9:22 AM, Peter Neher <[hidden email]> wrote:
I am using the precompiled 4.1. binaries under Ubuntu 12.4 (64 bit). Screenshot of the application attached. I also tried it with a diffusion weighted dataset loaded, but that didn't change anything.


On 05/29/2012 03:14 PM, Ron Kikinis wrote:
Did you try the nightly build? What platform?

On 5/29/12 9:08 AM, Peter Neher wrote:
Hi all,

I just wanted to check out the new whole brain tractography feature of
slicer 4 but the according module does not seem to contain any
functionality. Is this module still work in progress?

Best regards
Peter
_______________________________________________
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

_______________________________________________
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[hidden email]
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject


-- 
Dipl.-Inform. Peter Neher
German Cancer Research Centre
(DKFZ, Deutsches Krebsforschungszentrum in der Helmholtz-Gemeinschaft, Stiftung des öffentlichen Rechts)
Division of Medical and Biological Informatics
Im Neuenheimer Feld 280, D-69120 Heidelberg

Phone: 49-(0)6221-42-3552, Fax: 49-(0)6221-42-2345
E-Mail: [hidden email], Web: www.dkfz.de

The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message.

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Re: Whole Brain Tractography

Peter Neher
In reply to this post by Demian Wassermann-2
Thanks, this is working just fine!

Peter

On 05/30/2012 12:07 AM, Demian Wassermann wrote:

> Hello Peter,
>
> While we figure out what is wrong with the binary distribution, you replicate the wizard by hand:
>
> You can obtain the diffusion tensor image from your DICOM following the "SLICER4 DIFFUSION TENSOR IMAGING TUTORIAL" at
>
> http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Training
>
> Then if you use the labelmap seeding module without any mask, you will obtain a full brain tractography
>
> HTH
> Demian
>
> --
> Demian Wassermann, PhD
> [hidden email]
> LMI / PNL / SPL Labs
> Harvard Medical School
> Brigham and Women's Hospital
> 1249 Boylston, Boston, MA, USA
> http://lmi.bwh.harvard.edu/~wassermann/
>
> On May 29, 2012, at 9:08 AM, Peter Neher wrote:
>
>> Hi all,
>>
>> I just wanted to check out the new whole brain tractography feature of
>> slicer 4 but the according module does not seem to contain any
>> functionality. Is this module still work in progress?
>>
>> Best regards
>> Peter
>> _______________________________________________
>> 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

--
Dipl.-Inform. Peter Neher
German Cancer Research Centre
(DKFZ, Deutsches Krebsforschungszentrum in der Helmholtz-Gemeinschaft, Stiftung des öffentlichen Rechts)
Division of Medical and Biological Informatics
Im Neuenheimer Feld 280, D-69120 Heidelberg

Phone: 49-(0)6221-42-3552, Fax: 49-(0)6221-42-2345
E-Mail: [hidden email], Web: www.dkfz.de

The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message.

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Re: Whole Brain Tractography

Peter Neher
I have another question regarding the labelmap seeding. I wanted to use
a binary nrrd brain mask as seed image, but this image is not recognized
as labelmap. Is there a way to do that?

Best
Peter

On 05/30/2012 09:45 AM, Peter Neher wrote:

> Thanks, this is working just fine!
>
> Peter
>
> On 05/30/2012 12:07 AM, Demian Wassermann wrote:
>> Hello Peter,
>>
>> While we figure out what is wrong with the binary distribution, you replicate the wizard by hand:
>>
>> You can obtain the diffusion tensor image from your DICOM following the "SLICER4 DIFFUSION TENSOR IMAGING TUTORIAL" at
>>
>> http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Training
>>
>> Then if you use the labelmap seeding module without any mask, you will obtain a full brain tractography
>>
>> HTH
>> Demian
>>
>> --
>> Demian Wassermann, PhD
>> [hidden email]
>> LMI / PNL / SPL Labs
>> Harvard Medical School
>> Brigham and Women's Hospital
>> 1249 Boylston, Boston, MA, USA
>> http://lmi.bwh.harvard.edu/~wassermann/
>>
>> On May 29, 2012, at 9:08 AM, Peter Neher wrote:
>>
>>> Hi all,
>>>
>>> I just wanted to check out the new whole brain tractography feature of
>>> slicer 4 but the according module does not seem to contain any
>>> functionality. Is this module still work in progress?
>>>
>>> Best regards
>>> Peter
>>> _______________________________________________
>>> 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

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Re: Whole Brain Tractography

Kikinis, Ron,M.D.
in the add data dialog of slicer 4, click on options and then on label

On 5/30/12 10:59 AM, Peter Neher wrote:

> I have another question regarding the labelmap seeding. I wanted to use
> a binary nrrd brain mask as seed image, but this image is not recognized
> as labelmap. Is there a way to do that?
>
> Best
> Peter
>
> On 05/30/2012 09:45 AM, Peter Neher wrote:
>> Thanks, this is working just fine!
>>
>> Peter
>>
>> On 05/30/2012 12:07 AM, Demian Wassermann wrote:
>>> Hello Peter,
>>>
>>> While we figure out what is wrong with the binary distribution, you replicate the wizard by hand:
>>>
>>> You can obtain the diffusion tensor image from your DICOM following the "SLICER4 DIFFUSION TENSOR IMAGING TUTORIAL" at
>>>
>>> http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Training
>>>
>>> Then if you use the labelmap seeding module without any mask, you will obtain a full brain tractography
>>>
>>> HTH
>>> Demian
>>>
>>> --
>>> Demian Wassermann, PhD
>>> [hidden email]
>>> LMI / PNL / SPL Labs
>>> Harvard Medical School
>>> Brigham and Women's Hospital
>>> 1249 Boylston, Boston, MA, USA
>>> http://lmi.bwh.harvard.edu/~wassermann/
>>>
>>> On May 29, 2012, at 9:08 AM, Peter Neher wrote:
>>>
>>>> Hi all,
>>>>
>>>> I just wanted to check out the new whole brain tractography feature of
>>>> slicer 4 but the according module does not seem to contain any
>>>> functionality. Is this module still work in progress?
>>>>
>>>> Best regards
>>>> Peter
>>>> _______________________________________________
>>>> 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
>
> _______________________________________________
> 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

--
Ron Kikinis, M.D.,
Robert Greenes Distinguished Director of Biomedical Informatics
Professor of Radiology, Harvard Medical School
Director, Surgical Planning Laboratory
http://www.spl.harvard.edu/~kikinis
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Re: Whole Brain Tractography

Peter Neher
Thanks.

On 05/30/2012 07:31 PM, Ron Kikinis wrote:

> in the add data dialog of slicer 4, click on options and then on label
>
> On 5/30/12 10:59 AM, Peter Neher wrote:
>> I have another question regarding the labelmap seeding. I wanted to use
>> a binary nrrd brain mask as seed image, but this image is not recognized
>> as labelmap. Is there a way to do that?
>>
>> Best
>> Peter
>>
>> On 05/30/2012 09:45 AM, Peter Neher wrote:
>>> Thanks, this is working just fine!
>>>
>>> Peter
>>>
>>> On 05/30/2012 12:07 AM, Demian Wassermann wrote:
>>>> Hello Peter,
>>>>
>>>> While we figure out what is wrong with the binary distribution, you replicate the wizard by hand:
>>>>
>>>> You can obtain the diffusion tensor image from your DICOM following the "SLICER4 DIFFUSION TENSOR IMAGING TUTORIAL" at
>>>>
>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Training
>>>>
>>>> Then if you use the labelmap seeding module without any mask, you will obtain a full brain tractography
>>>>
>>>> HTH
>>>> Demian
>>>>
>>>> --
>>>> Demian Wassermann, PhD
>>>> [hidden email]
>>>> LMI / PNL / SPL Labs
>>>> Harvard Medical School
>>>> Brigham and Women's Hospital
>>>> 1249 Boylston, Boston, MA, USA
>>>> http://lmi.bwh.harvard.edu/~wassermann/
>>>>
>>>> On May 29, 2012, at 9:08 AM, Peter Neher wrote:
>>>>
>>>>> Hi all,
>>>>>
>>>>> I just wanted to check out the new whole brain tractography feature of
>>>>> slicer 4 but the according module does not seem to contain any
>>>>> functionality. Is this module still work in progress?
>>>>>
>>>>> Best regards
>>>>> Peter
>>>>> _______________________________________________
>>>>> 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
>> _______________________________________________
>> 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

--
Dipl.-Inform. Peter Neher
German Cancer Research Centre
(DKFZ, Deutsches Krebsforschungszentrum in der Helmholtz-Gemeinschaft, Stiftung des öffentlichen Rechts)
Division of Medical and Biological Informatics
Im Neuenheimer Feld 280, D-69120 Heidelberg

Phone: 49-(0)6221-42-3552, Fax: 49-(0)6221-42-2345
E-Mail: [hidden email], Web: www.dkfz.de

The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message.

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Re: Whole Brain Tractography

Peter Neher
In reply to this post by Kikinis, Ron,M.D.
The tracking worked fine now, but when I tried to load the results in an
external viewer the tracking seems to be mirrored around the x and y
axis. I compared the fiber bundle generated by slicer to the mask image
as well as to tracking results from other toolkits. The only object that
is not aligned correctly seems to be the slicer tracking result. The
attached images illustrate the mirroring problem. You can see a surface
mesh generated from the mask image and the slicer tracking result. The
two objects fit fine after manually mirroring the mask image (screenshot
2). Is there any known issue like that?

Best
Peter

On 05/30/2012 07:31 PM, Ron Kikinis wrote:

> in the add data dialog of slicer 4, click on options and then on label
>
> On 5/30/12 10:59 AM, Peter Neher wrote:
>> I have another question regarding the labelmap seeding. I wanted to use
>> a binary nrrd brain mask as seed image, but this image is not recognized
>> as labelmap. Is there a way to do that?
>>
>> Best
>> Peter
>>
>> On 05/30/2012 09:45 AM, Peter Neher wrote:
>>> Thanks, this is working just fine!
>>>
>>> Peter
>>>
>>> On 05/30/2012 12:07 AM, Demian Wassermann wrote:
>>>> Hello Peter,
>>>>
>>>> While we figure out what is wrong with the binary distribution, you replicate the wizard by hand:
>>>>
>>>> You can obtain the diffusion tensor image from your DICOM following the "SLICER4 DIFFUSION TENSOR IMAGING TUTORIAL" at
>>>>
>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Training
>>>>
>>>> Then if you use the labelmap seeding module without any mask, you will obtain a full brain tractography
>>>>
>>>> HTH
>>>> Demian
>>>>
>>>> --
>>>> Demian Wassermann, PhD
>>>> [hidden email]
>>>> LMI / PNL / SPL Labs
>>>> Harvard Medical School
>>>> Brigham and Women's Hospital
>>>> 1249 Boylston, Boston, MA, USA
>>>> http://lmi.bwh.harvard.edu/~wassermann/
>>>>
>>>> On May 29, 2012, at 9:08 AM, Peter Neher wrote:
>>>>
>>>>> Hi all,
>>>>>
>>>>> I just wanted to check out the new whole brain tractography feature of
>>>>> slicer 4 but the according module does not seem to contain any
>>>>> functionality. Is this module still work in progress?
>>>>>
>>>>> Best regards
>>>>> Peter
>>>>> _______________________________________________
>>>>> 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
>> _______________________________________________
>> 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
--
Dipl.-Inform. Peter Neher
German Cancer Research Centre
(DKFZ, Deutsches Krebsforschungszentrum in der Helmholtz-Gemeinschaft, Stiftung des öffentlichen Rechts)
Division of Medical and Biological Informatics
Im Neuenheimer Feld 280, D-69120 Heidelberg

Phone: 49-(0)6221-42-3552, Fax: 49-(0)6221-42-2345
E-Mail: [hidden email], Web: www.dkfz.de

The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message.


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slicer_tracking_and_mask.png (3M) Download Attachment
slicer_tracking_and_mirrored_mask.png (3M) Download Attachment
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Re: Whole Brain Tractography

Steve Pieper
Hi Peter -

Slicer's tracts and models will be in RAS coordinates [1].  Chances are that your other tool uses LPS, so the left/right and anterior/posterior directions would be incorrect if this difference is not taken into account.

-Steve


[1] http://www.slicer.org/slicerWiki/index.php/Coordinate_systems

On Thu, May 31, 2012 at 7:38 AM, Peter Neher <[hidden email]> wrote:
The tracking worked fine now, but when I tried to load the results in an external viewer the tracking seems to be mirrored around the x and y axis. I compared the fiber bundle generated by slicer to the mask image as well as to tracking results from other toolkits. The only object that is not aligned correctly seems to be the slicer tracking result. The attached images illustrate the mirroring problem. You can see a surface mesh generated from the mask image and the slicer tracking result. The two objects fit fine after manually mirroring the mask image (screenshot 2). Is there any known issue like that?

Best
Peter

On 05/30/2012 07:31 PM, Ron Kikinis wrote:
in the add data dialog of slicer 4, click on options and then on label

On 5/30/12 10:59 AM, Peter Neher wrote:
I have another question regarding the labelmap seeding. I wanted to use
a binary nrrd brain mask as seed image, but this image is not recognized
as labelmap. Is there a way to do that?

Best
Peter

On 05/30/2012 09:45 AM, Peter Neher wrote:
Thanks, this is working just fine!

Peter

On 05/30/2012 12:07 AM, Demian Wassermann wrote:
Hello Peter,

While we figure out what is wrong with the binary distribution, you replicate the wizard by hand:

You can obtain the diffusion tensor image from your DICOM following the "SLICER4 DIFFUSION TENSOR IMAGING TUTORIAL" at

http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Training

Then if you use the labelmap seeding module without any mask, you will obtain a full brain tractography

HTH
Demian

--
Demian Wassermann, PhD
[hidden email]
LMI / PNL / SPL Labs
Harvard Medical School
Brigham and Women's Hospital
1249 Boylston, Boston, MA, USA
http://lmi.bwh.harvard.edu/~wassermann/

On May 29, 2012, at 9:08 AM, Peter Neher wrote:

Hi all,

I just wanted to check out the new whole brain tractography feature of
slicer 4 but the according module does not seem to contain any
functionality. Is this module still work in progress?

Best regards
Peter
_______________________________________________
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject

--
Dipl.-Inform. Peter Neher
German Cancer Research Centre
(DKFZ, Deutsches Krebsforschungszentrum in der Helmholtz-Gemeinschaft, Stiftung des öffentlichen Rechts)
Division of Medical and Biological Informatics
Im Neuenheimer Feld 280, D-69120 Heidelberg

Phone: 49-(0)6221-42-3552, Fax: 49-(0)6221-42-2345
E-Mail: [hidden email], Web: www.dkfz.de

The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message.


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Re: Whole Brain Tractography

Peter Neher
Hi Steve,

that seems to be the problem. The image I used for the tracking uses LPS but the resulting fiber bundle uses RAS. So flipping the fiber bundle manually seems to be the only solution.

Best
Peter

On 05/31/2012 01:58 PM, Steve Pieper wrote:
Hi Peter -

Slicer's tracts and models will be in RAS coordinates [1].  Chances are that your other tool uses LPS, so the left/right and anterior/posterior directions would be incorrect if this difference is not taken into account.

-Steve


[1] http://www.slicer.org/slicerWiki/index.php/Coordinate_systems

On Thu, May 31, 2012 at 7:38 AM, Peter Neher <[hidden email]> wrote:
The tracking worked fine now, but when I tried to load the results in an external viewer the tracking seems to be mirrored around the x and y axis. I compared the fiber bundle generated by slicer to the mask image as well as to tracking results from other toolkits. The only object that is not aligned correctly seems to be the slicer tracking result. The attached images illustrate the mirroring problem. You can see a surface mesh generated from the mask image and the slicer tracking result. The two objects fit fine after manually mirroring the mask image (screenshot 2). Is there any known issue like that?

Best
Peter

On 05/30/2012 07:31 PM, Ron Kikinis wrote:
in the add data dialog of slicer 4, click on options and then on label

On 5/30/12 10:59 AM, Peter Neher wrote:
I have another question regarding the labelmap seeding. I wanted to use
a binary nrrd brain mask as seed image, but this image is not recognized
as labelmap. Is there a way to do that?

Best
Peter

On 05/30/2012 09:45 AM, Peter Neher wrote:
Thanks, this is working just fine!

Peter

On 05/30/2012 12:07 AM, Demian Wassermann wrote:
Hello Peter,

While we figure out what is wrong with the binary distribution, you replicate the wizard by hand:

You can obtain the diffusion tensor image from your DICOM following the "SLICER4 DIFFUSION TENSOR IMAGING TUTORIAL" at

http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Training

Then if you use the labelmap seeding module without any mask, you will obtain a full brain tractography

HTH
Demian

--
Demian Wassermann, PhD
[hidden email]
LMI / PNL / SPL Labs
Harvard Medical School
Brigham and Women's Hospital
1249 Boylston, Boston, MA, USA
http://lmi.bwh.harvard.edu/~wassermann/

On May 29, 2012, at 9:08 AM, Peter Neher wrote:

Hi all,

I just wanted to check out the new whole brain tractography feature of
slicer 4 but the according module does not seem to contain any
functionality. Is this module still work in progress?

Best regards
Peter
_______________________________________________
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
_______________________________________________
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

--
Dipl.-Inform. Peter Neher
German Cancer Research Centre
(DKFZ, Deutsches Krebsforschungszentrum in der Helmholtz-Gemeinschaft, Stiftung des öffentlichen Rechts)
Division of Medical and Biological Informatics
Im Neuenheimer Feld 280, D-69120 Heidelberg

Phone: 49-(0)6221-42-3552, Fax: 49-(0)6221-42-2345
E-Mail: [hidden email], Web: www.dkfz.de

The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message.


_______________________________________________
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


-- 
Dipl.-Inform. Peter Neher
German Cancer Research Centre
(DKFZ, Deutsches Krebsforschungszentrum in der Helmholtz-Gemeinschaft, Stiftung des öffentlichen Rechts)
Division of Medical and Biological Informatics
Im Neuenheimer Feld 280, D-69120 Heidelberg

Phone: 49-(0)6221-42-3552, Fax: 49-(0)6221-42-2345
E-Mail: [hidden email], Web: www.dkfz.de

The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message.

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Models from grayscale modelmaker

Murat Maga

Hi,

 

Is there any reason why the models from grayscale model maker shows up under the Annotations menu, instead of the Models trees?  Is there something unique about them as oppose to creating the model from the label editor?

 

Slicer also fails miserably when I click the edit button next to the model name under the ROI hierarchy? I am using version Slicer 4.1.0-2012-05-16 under windows 7 64 bit.

 

M

 

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Peter Neher
Sent: Thursday, May 31, 2012 5:50 AM
To: [hidden email]
Subject: Re: [slicer-users] Whole Brain Tractography

 

Hi Steve,

that seems to be the problem. The image I used for the tracking uses LPS but the resulting fiber bundle uses RAS. So flipping the fiber bundle manually seems to be the only solution.

Best
Peter

On 05/31/2012 01:58 PM, Steve Pieper wrote:

Hi Peter -

Slicer's tracts and models will be in RAS coordinates [1].  Chances are that your other tool uses LPS, so the left/right and anterior/posterior directions would be incorrect if this difference is not taken into account.

-Steve


[1] http://www.slicer.org/slicerWiki/index.php/Coordinate_systems

On Thu, May 31, 2012 at 7:38 AM, Peter Neher <[hidden email]> wrote:

The tracking worked fine now, but when I tried to load the results in an external viewer the tracking seems to be mirrored around the x and y axis. I compared the fiber bundle generated by slicer to the mask image as well as to tracking results from other toolkits. The only object that is not aligned correctly seems to be the slicer tracking result. The attached images illustrate the mirroring problem. You can see a surface mesh generated from the mask image and the slicer tracking result. The two objects fit fine after manually mirroring the mask image (screenshot 2). Is there any known issue like that?

Best
Peter


On 05/30/2012 07:31 PM, Ron Kikinis wrote:

in the add data dialog of slicer 4, click on options and then on label

On 5/30/12 10:59 AM, Peter Neher wrote:

I have another question regarding the labelmap seeding. I wanted to use
a binary nrrd brain mask as seed image, but this image is not recognized
as labelmap. Is there a way to do that?

Best
Peter

On 05/30/2012 09:45 AM, Peter Neher wrote:

Thanks, this is working just fine!

Peter

On 05/30/2012 12:07 AM, Demian Wassermann wrote:

Hello Peter,

While we figure out what is wrong with the binary distribution, you replicate the wizard by hand:

You can obtain the diffusion tensor image from your DICOM following the "SLICER4 DIFFUSION TENSOR IMAGING TUTORIAL" at

http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Training

Then if you use the labelmap seeding module without any mask, you will obtain a full brain tractography

HTH
Demian

--
Demian Wassermann, PhD
[hidden email]
LMI / PNL / SPL Labs
Harvard Medical School
Brigham and Women's Hospital
1249 Boylston, Boston, MA, USA
http://lmi.bwh.harvard.edu/~wassermann/

On May 29, 2012, at 9:08 AM, Peter Neher wrote:

Hi all,

I just wanted to check out the new whole brain tractography feature of
slicer 4 but the according module does not seem to contain any
functionality. Is this module still work in progress?

Best regards
Peter
_______________________________________________
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

_______________________________________________
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


--

Dipl.-Inform. Peter Neher
German Cancer Research Centre
(DKFZ, Deutsches Krebsforschungszentrum in der Helmholtz-Gemeinschaft, Stiftung des öffentlichen Rechts)
Division of Medical and Biological Informatics
Im Neuenheimer Feld 280, D-69120 Heidelberg

Phone: 49-(0)6221-42-3552, Fax: 49-(0)6221-42-2345
E-Mail: [hidden email], Web: www.dkfz.de

The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message.


_______________________________________________
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

 



-- 
Dipl.-Inform. Peter Neher
German Cancer Research Centre
(DKFZ, Deutsches Krebsforschungszentrum in der Helmholtz-Gemeinschaft, Stiftung des öffentlichen Rechts)
Division of Medical and Biological Informatics
Im Neuenheimer Feld 280, D-69120 Heidelberg
 
Phone: 49-(0)6221-42-3552, Fax: 49-(0)6221-42-2345
E-Mail: [hidden email], Web: www.dkfz.de
 
The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message.

_______________________________________________
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Re: Models from grayscale modelmaker

Aucoin, Nicole
Hi Murat,

On return from the label map model maker, Slicer loads in a mrml file
that can contain multiple models, while the greyscale one results in a
model file directly being loaded.
I can't reproduce either of these reported behaviours. Did you create an
ROI first and then run the greyscale model maker? Did you create a new
output model or select an annotation model?
Can you be more specific about "failing miserably"? What was the model
name you were trying to edit? Was it the output of the model maker by
any chance?
If you can reliably reproduce these problems, please enter a bug report
with sample data if possible.

thanks,
Nicole


On 06/01/2012 05:13 PM, Murat Maga wrote:

>
> Hi,
>
> Is there any reason why the models from grayscale model maker shows up
> under the Annotations menu, instead of the Models trees?  Is there
> something unique about them as oppose to creating the model from the
> label editor?
>
> Slicer also fails miserably when I click the edit button next to the
> model name under the ROI hierarchy? I am using version Slicer
> 4.1.0-2012-05-16 under windows 7 64 bit.
>
> M
>
>

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