Tensor Orientation Colors

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Tensor Orientation Colors

Douglas Rowland
Hi,
I am new to 3D Slicer and DTI. I acquired ex vivo spinal cord data on Bruker 7T scanner. I used DSI Studio to process the data into FSL nifti format in order to get diffusion data into 3D Slicer and perform the tensor estimation. I have run into a problem with orientation. The spin Head-Foot is oriented along the A-P axis in slicer and the A-P is along the H-F. When the tensor is estimated the White matter tracks in the spinal cord are color labeled as A-P (green) instead of H-F (blue).

Is there anyway to reorient the diffusion data or the DTI data to get the proper color orientation?

Thanks

Doug



------------------------------------
Douglas J Rowland, Ph.D.
Principal Research Scientist, Center for Molecular and Genomic Imaging
Co-Director Animal Imaging Shared Resource, UCD Comprehensive Cancer Center
University of California, Davis

Office:  (530) 754 - 8960
Lab:     (530) 754 - 6633
Fax:     (530) 754 - 5739
imaging.bme.ucdavis.edu

US Postal Service:
Biomedical Engineering
University of California
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Davis, CA 95616

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Re: Tensor Orientation Colors

Fernando Pérez-García
Hi Douglas,

I don't know much about diffusion imaging so I might be wrong, but I think you have two options:
 - Apply a transform to your dMRI to change your image orientation and apply the same transform to its bvec
 - Apply a transform to your DTI image and the same transform to the three values of each voxel. I have recently written a small function that applies this transformation to a displacement field, so I might be able to help with that.


Best,

Fernando

2016-12-08 1:48 GMT+01:00 Douglas J Rowland <[hidden email]>:
Hi,
I am new to 3D Slicer and DTI. I acquired ex vivo spinal cord data on Bruker 7T scanner. I used DSI Studio to process the data into FSL nifti format in order to get diffusion data into 3D Slicer and perform the tensor estimation. I have run into a problem with orientation. The spin Head-Foot is oriented along the A-P axis in slicer and the A-P is along the H-F. When the tensor is estimated the White matter tracks in the spinal cord are color labeled as A-P (green) instead of H-F (blue).

Is there anyway to reorient the diffusion data or the DTI data to get the proper color orientation?

Thanks

Doug



------------------------------------
Douglas J Rowland, Ph.D.
Principal Research Scientist, Center for Molecular and Genomic Imaging
Co-Director Animal Imaging Shared Resource, UCD Comprehensive Cancer Center
University of California, Davis

Office:  <a href="tel:%28530%29%20754%20-%208960" value="&#43;15307548960">(530) 754 - 8960
Lab:     <a href="tel:%28530%29%20754%20-%206633" value="&#43;15307546633">(530) 754 - 6633
Fax:     <a href="tel:%28530%29%20754%20-%205739" value="&#43;15307545739">(530) 754 - 5739
imaging.bme.ucdavis.edu

US Postal Service:
Biomedical Engineering
University of California
One Shields Avenue
Davis, CA 95616

Courier:
Biomedical Engineering
Genome and Biomedical Sciences Facility, 0300
451 Health Sciences Drive
Davis, CA 95616

_______________________________________________
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[hidden email]
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


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Re: Tensor Orientation Colors

inorton
In reply to this post by Douglas Rowland
Can you share an example dataset? There are a number of issues with nifti compatibility among various software packages, unfortunately.

(Out of curiosity, what do you want to do in Slicer that can't be done in DSI Studio?)

On Wed, Dec 7, 2016 at 7:48 PM, Douglas J Rowland <[hidden email]> wrote:
Hi,
I am new to 3D Slicer and DTI. I acquired ex vivo spinal cord data on Bruker 7T scanner. I used DSI Studio to process the data into FSL nifti format in order to get diffusion data into 3D Slicer and perform the tensor estimation. I have run into a problem with orientation. The spin Head-Foot is oriented along the A-P axis in slicer and the A-P is along the H-F. When the tensor is estimated the White matter tracks in the spinal cord are color labeled as A-P (green) instead of H-F (blue).

Is there anyway to reorient the diffusion data or the DTI data to get the proper color orientation?

Thanks

Doug



------------------------------------
Douglas J Rowland, Ph.D.
Principal Research Scientist, Center for Molecular and Genomic Imaging
Co-Director Animal Imaging Shared Resource, UCD Comprehensive Cancer Center
University of California, Davis

Office:  <a href="tel:%28530%29%20754%20-%208960" value="&#43;15307548960">(530) 754 - 8960
Lab:     <a href="tel:%28530%29%20754%20-%206633" value="&#43;15307546633">(530) 754 - 6633
Fax:     <a href="tel:%28530%29%20754%20-%205739" value="&#43;15307545739">(530) 754 - 5739
imaging.bme.ucdavis.edu

US Postal Service:
Biomedical Engineering
University of California
One Shields Avenue
Davis, CA 95616

Courier:
Biomedical Engineering
Genome and Biomedical Sciences Facility, 0300
451 Health Sciences Drive
Davis, CA 95616

_______________________________________________
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


_______________________________________________
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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Re: Tensor Orientation Colors

Douglas Rowland
In reply to this post by Douglas Rowland
Hi Isaiah and Fernando,
Thank you for the impute. I was thinking that the transformation might need to be applied to the bevcs as well. Thanks Fernando for that important point. 

In the end I am able to use DSI studio to transform the data and it also transforms the bvecs. So I am able to import the data into Slicer and get the correct color orientations now. 

I was originally trying to reorient the data in slicer. There are two modules that I thought would work to reorient the data and associated bvecs or the DTI data itself. These are Resample scalar/vector/DWI volume and Resample DTI volume. I was able to resample the DWI volumes but I don’t think the bvecs were transformed. The color orientations did not change. When I used the resample DTI on a DTI volume, the program crashed. This may have been a result of the file size though. It is a high resolution dataset (DWI data about 1Gb). 

So I am not sure if it is a bug in Slicer or I am just using it wrong. 

Regarding Slicer vs DSI studio usage, I am trying not to fragment my workspace to much. I found the tutorials for Slicer to be extremely helpful in getting started with DTI reconstruction, viewing and analysis of the data. So I became more comfortable working the slicer workspace. As I get more comfortable working with DTI data, I might explore the functionality of DSI studio a bit more. 

Thanks

Doug

On Dec 9, 2016, at 6:44 AM, Isaiah Norton <[hidden email]> wrote:

Can you share an example dataset? There are a number of issues with nifti compatibility among various software packages, unfortunately.

(Out of curiosity, what do you want to do in Slicer that can't be done in DSI Studio?)

On Wed, Dec 7, 2016 at 7:48 PM, Douglas J Rowland <[hidden email]> wrote:
Hi,
I am new to 3D Slicer and DTI. I acquired ex vivo spinal cord data on Bruker 7T scanner. I used DSI Studio to process the data into FSL nifti format in order to get diffusion data into 3D Slicer and perform the tensor estimation. I have run into a problem with orientation. The spin Head-Foot is oriented along the A-P axis in slicer and the A-P is along the H-F. When the tensor is estimated the White matter tracks in the spinal cord are color labeled as A-P (green) instead of H-F (blue).

Is there anyway to reorient the diffusion data or the DTI data to get the proper color orientation?

Thanks

Doug



------------------------------------
Douglas J Rowland, Ph.D.
Principal Research Scientist, Center for Molecular and Genomic Imaging
Co-Director Animal Imaging Shared Resource, UCD Comprehensive Cancer Center
University of California, Davis

Office:  <a href="tel:%28530%29%20754%20-%208960" value="&#43;15307548960" class="">(530) 754 - 8960
Lab:     <a href="tel:%28530%29%20754%20-%206633" value="&#43;15307546633" class="">(530) 754 - 6633
Fax:     <a href="tel:%28530%29%20754%20-%205739" value="&#43;15307545739" class="">(530) 754 - 5739
imaging.bme.ucdavis.edu

US Postal Service:
Biomedical Engineering
University of California
One Shields Avenue
Davis, CA 95616

Courier:
Biomedical Engineering
Genome and Biomedical Sciences Facility, 0300
451 Health Sciences Drive
Davis, CA 95616

_______________________________________________
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



_______________________________________________
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[hidden email]
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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Re: Tensor Orientation Colors

inorton
In reply to this post by Douglas Rowland
Hi Doug,

Great that you found a solution. I believe there is a large update coming to DWIConvert coming which will improve nifti diffusion data support in the future. I'm not sure about the Resampling modules, unfortunately, as we don't generally use them in our workflow.

Best,
Isaiah

On Fri, Dec 9, 2016 at 12:30 PM, Douglas J Rowland <[hidden email]> wrote:
Hi Isaiah and Fernando,
Thank you for the impute. I was thinking that the transformation might need to be applied to the bevcs as well. Thanks Fernando for that important point. 

In the end I am able to use DSI studio to transform the data and it also transforms the bvecs. So I am able to import the data into Slicer and get the correct color orientations now. 

I was originally trying to reorient the data in slicer. There are two modules that I thought would work to reorient the data and associated bvecs or the DTI data itself. These are Resample scalar/vector/DWI volume and Resample DTI volume. I was able to resample the DWI volumes but I don’t think the bvecs were transformed. The color orientations did not change. When I used the resample DTI on a DTI volume, the program crashed. This may have been a result of the file size though. It is a high resolution dataset (DWI data about 1Gb). 

So I am not sure if it is a bug in Slicer or I am just using it wrong. 

Regarding Slicer vs DSI studio usage, I am trying not to fragment my workspace to much. I found the tutorials for Slicer to be extremely helpful in getting started with DTI reconstruction, viewing and analysis of the data. So I became more comfortable working the slicer workspace. As I get more comfortable working with DTI data, I might explore the functionality of DSI studio a bit more. 

Thanks

Doug

On Dec 9, 2016, at 6:44 AM, Isaiah Norton <[hidden email]> wrote:

Can you share an example dataset? There are a number of issues with nifti compatibility among various software packages, unfortunately.

(Out of curiosity, what do you want to do in Slicer that can't be done in DSI Studio?)

On Wed, Dec 7, 2016 at 7:48 PM, Douglas J Rowland <[hidden email]> wrote:
Hi,
I am new to 3D Slicer and DTI. I acquired ex vivo spinal cord data on Bruker 7T scanner. I used DSI Studio to process the data into FSL nifti format in order to get diffusion data into 3D Slicer and perform the tensor estimation. I have run into a problem with orientation. The spin Head-Foot is oriented along the A-P axis in slicer and the A-P is along the H-F. When the tensor is estimated the White matter tracks in the spinal cord are color labeled as A-P (green) instead of H-F (blue).

Is there anyway to reorient the diffusion data or the DTI data to get the proper color orientation?

Thanks

Doug



------------------------------------
Douglas J Rowland, Ph.D.
Principal Research Scientist, Center for Molecular and Genomic Imaging
Co-Director Animal Imaging Shared Resource, UCD Comprehensive Cancer Center
University of California, Davis

Office:  <a href="tel:%28530%29%20754%20-%208960" value="&#43;15307548960" target="_blank"> (530) 754 - 8960
Lab:     <a href="tel:%28530%29%20754%20-%206633" value="&#43;15307546633" target="_blank">(530) 754 - 6633
Fax:     <a href="tel:%28530%29%20754%20-%205739" value="&#43;15307545739" target="_blank">(530) 754 - 5739
imaging.bme.ucdavis.edu

US Postal Service:
Biomedical Engineering
University of California
One Shields Avenue
Davis, CA 95616

Courier:
Biomedical Engineering
Genome and Biomedical Sciences Facility, 0300
451 Health Sciences Drive
Davis, CA 95616

_______________________________________________
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




_______________________________________________
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[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