DWI to DTI convertion

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DWI to DTI convertion

Cyril Jaudet
Hello Slicer Community,
I want to work with the diffusion module of Slicr but i have some problem.
We perform DWI acquisitions with a siemens Skyra. After acquisition i use DWIconverter on two series. An anonymise version can be download with the link:
https://drive.google.com/drive/folders/0BxFtS_SN_AZPYzQ2T3czWk9LQms?usp=sharing

Acq1 is working fine but Acq2 give an error :

E: can't change to unencapsulated representation for pixel data

E: can't determine 'PhotometricInterpretation' of decompressed image

Error: no DICOMfiles found in inputDirectory:


I don't understand what i am doing wrong and if there is a way to fixe it.

Thank you,


Cyril Jaudet, PhD

UZburssel




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Re: DWI to DTI convertion

inorton
Hi Cyril,

The difference is that the second acquisition is encoded using lossless JPEG transfer syntax:

15c15
< # Used TransferSyntax: Little Endian Explicit
---
> # Used TransferSyntax: JPEG Lossless, Non-hierarchical, 1st Order Prediction

Currently the codecs required to read such files are not registered early enough to be used when DWIConvert is parsing the file list. I've submitted a fix here:


However, I'm not sure if/when the Slicer version of BRAINSTools will be updated to use this change (if accepted). So for now you can either change settings on the scanner to avoid using JPEG compression in the second acquisition protocol, or possibly compile a version of Slicer yourself with the above-mentioned change applied locally.

Best,
Isaiah



On Mon, Nov 28, 2016 at 4:09 AM, Cyril Jaudet <[hidden email]> wrote:
Hello Slicer Community,
I want to work with the diffusion module of Slicr but i have some problem.
We perform DWI acquisitions with a siemens Skyra. After acquisition i use DWIconverter on two series. An anonymise version can be download with the link:
https://drive.google.com/drive/folders/0BxFtS_SN_AZPYzQ2T3czWk9LQms?usp=sharing

Acq1 is working fine but Acq2 give an error :

E: can't change to unencapsulated representation for pixel data

E: can't determine 'PhotometricInterpretation' of decompressed image

Error: no DICOMfiles found in inputDirectory:


I don't understand what i am doing wrong and if there is a way to fixe it.

Thank you,


Cyril Jaudet, PhD

UZburssel




_______________________________________________
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
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Re: DWI to DTI convertion

Cyril Jaudet
In reply to this post by Cyril Jaudet

Thanks you Isaiah   I ll try to compile braintool as standalone to perform the conversion with the right option.
Cyril


Le 28 nov. 2016 5:57 PM, "Isaiah Norton" <[hidden email]> a écrit :
Hi Cyril,

The difference is that the second acquisition is encoded using lossless JPEG transfer syntax:

15c15
< # Used TransferSyntax: Little Endian Explicit
---
> # Used TransferSyntax: JPEG Lossless, Non-hierarchical, 1st Order Prediction

Currently the codecs required to read such files are not registered early enough to be used when DWIConvert is parsing the file list. I've submitted a fix here:


However, I'm not sure if/when the Slicer version of BRAINSTools will be updated to use this change (if accepted). So for now you can either change settings on the scanner to avoid using JPEG compression in the second acquisition protocol, or possibly compile a version of Slicer yourself with the above-mentioned change applied locally.

Best,
Isaiah



On Mon, Nov 28, 2016 at 4:09 AM, Cyril Jaudet <[hidden email]> wrote:
Hello Slicer Community,
I want to work with the diffusion module of Slicr but i have some problem.
We perform DWI acquisitions with a siemens Skyra. After acquisition i use DWIconverter on two series. An anonymise version can be download with the link:
https://drive.google.com/drive/folders/0BxFtS_SN_AZPYzQ2T3czWk9LQms?usp=sharing

Acq1 is working fine but Acq2 give an error :

E: can't change to unencapsulated representation for pixel data

E: can't determine 'PhotometricInterpretation' of decompressed image

Error: no DICOMfiles found in inputDirectory:


I don't understand what i am doing wrong and if there is a way to fixe it.

Thank you,


Cyril Jaudet, PhD

UZburssel




_______________________________________________
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
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Re: DWI to DTI convertion

Cyril Jaudet
In reply to this post by Cyril Jaudet
Dag Isaiah,
i find an alternative solution. I use OSIRIX to decompress the image in an adapted dicom format.
Thank you for the help. Have a nice evening,
Cyril

2016-11-28 21:53 GMT+01:00 Cyril Jaudet <[hidden email]>:

Thanks you Isaiah   I ll try to compile braintool as standalone to perform the conversion with the right option.
Cyril


Le 28 nov. 2016 5:57 PM, "Isaiah Norton" <[hidden email]> a écrit :
Hi Cyril,

The difference is that the second acquisition is encoded using lossless JPEG transfer syntax:

15c15
< # Used TransferSyntax: Little Endian Explicit
---
> # Used TransferSyntax: JPEG Lossless, Non-hierarchical, 1st Order Prediction

Currently the codecs required to read such files are not registered early enough to be used when DWIConvert is parsing the file list. I've submitted a fix here:


However, I'm not sure if/when the Slicer version of BRAINSTools will be updated to use this change (if accepted). So for now you can either change settings on the scanner to avoid using JPEG compression in the second acquisition protocol, or possibly compile a version of Slicer yourself with the above-mentioned change applied locally.

Best,
Isaiah



On Mon, Nov 28, 2016 at 4:09 AM, Cyril Jaudet <[hidden email]> wrote:
Hello Slicer Community,
I want to work with the diffusion module of Slicr but i have some problem.
We perform DWI acquisitions with a siemens Skyra. After acquisition i use DWIconverter on two series. An anonymise version can be download with the link:
https://drive.google.com/drive/folders/0BxFtS_SN_AZPYzQ2T3czWk9LQms?usp=sharing

Acq1 is working fine but Acq2 give an error :

E: can't change to unencapsulated representation for pixel data

E: can't determine 'PhotometricInterpretation' of decompressed image

Error: no DICOMfiles found in inputDirectory:


I don't understand what i am doing wrong and if there is a way to fixe it.

Thank you,


Cyril Jaudet, PhD

UZburssel




_______________________________________________
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