Problem with opening DWI series

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Problem with opening DWI series

krzys59
I tried create tractography like tutorial. I have series of dicom https://www.dropbox.com/s/vhidw6qlws8o14m/anonym.zip?dl=0
It was named DWI AX ....
Openig series is with errors:
Images are not equally spaced (a difference of 6.00002 in spacings was detected).  Slicer will load this series as if it had a spacing of 0.  Please use caution.
Next I tried used Volume, and set DWI Component, but I dont see this option. I tried following as is described in tutorial: DiffusionMRIanalysis_Tutorial_SoniaPujol_2013 (all works fine if I used exemple date)
Could you tell me, how can I repair my series DWI? Or maybe it is useless series?
Series looks like dicom, but not DWI? Is possible to use this series to create tractography?
Regards
Krzysztof

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Re: Problem with opening DWI series

Andrey Fedorov-2
Hi,

it seems that your DWI dataset is being loaded as a scalar volume.
This will NOT work, it must be loaded as DWI.

I do not work with DWI and don't know the current and recommended
process (I would hope that the tutorial you are following should have
it described, but I just don't know, and it doesn't sound like it
does). You may want to look into using DWConvert on your data first,
but, again, I do not know whether Slicer has the proper version of
DWConvert.

If you follow the proper process, you may be able to load this
dataset, but I defer to the DWI experts to describe what the proper
process is.

AF

On Sat, Oct 3, 2015 at 2:57 PM, Krzysztof Grandys
<[hidden email]> wrote:

> I tried create tractography like tutorial. I have series of dicom
> https://www.dropbox.com/s/vhidw6qlws8o14m/anonym.zip?dl=0
> It was named DWI AX ....
> Openig series is with errors:
> Images are not equally spaced (a difference of 6.00002 in spacings was
> detected).  Slicer will load this series as if it had a spacing of 0.
> Please use caution.
> Next I tried used Volume, and set DWI Component, but I dont see this option.
> I tried following as is described in tutorial:
> DiffusionMRIanalysis_Tutorial_SoniaPujol_2013 (all works fine if I used
> exemple date)
> Could you tell me, how can I repair my series DWI? Or maybe it is useless
> series?
> Series looks like dicom, but not DWI? Is possible to use this series to
> create tractography?
> Regards
> Krzysztof
>
> _______________________________________________
> 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
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
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Re: Problem with opening DWI series

krzys59
In reply to this post by krzys59
Thank you for respods
Your right, this is not DWI, despite its name.
I create full zip with anonymous mri examination https://www.dropbox.com/s/bb65pj5etfk53mc/Anonymous_MRI.zip?dl=0
This is boy with vary small tumor, hi is after operation, but i`d like create visualisation with tractography. Simple visualisation from CT and angioCT I created without problems (link to avi https://drive.google.com/open?id=0Bxtky_PLNA2SQmdwVGNmX1NQRTg)
Could you explain my how I can do that using my dicom series. Or maybe, from this series it is not possible?
I tried do this like is described in tutorial "Slicer4 Diffusion Tensor Imaging Tutorial" but can`t a valid DWI series in my example.
I`m not radiologist
Krzysztof

2015-10-04 4:09 GMT+02:00 Andrey Fedorov <[hidden email]>:
Hi,

it seems that your DWI dataset is being loaded as a scalar volume.
This will NOT work, it must be loaded as DWI.

I do not work with DWI and don't know the current and recommended
process (I would hope that the tutorial you are following should have
it described, but I just don't know, and it doesn't sound like it
does). You may want to look into using DWConvert on your data first,
but, again, I do not know whether Slicer has the proper version of
DWConvert.

If you follow the proper process, you may be able to load this
dataset, but I defer to the DWI experts to describe what the proper
process is.

AF

On Sat, Oct 3, 2015 at 2:57 PM, Krzysztof Grandys
<[hidden email]> wrote:
> I tried create tractography like tutorial. I have series of dicom
> https://www.dropbox.com/s/vhidw6qlws8o14m/anonym.zip?dl=0
> It was named DWI AX ....
> Openig series is with errors:
> Images are not equally spaced (a difference of 6.00002 in spacings was
> detected).  Slicer will load this series as if it had a spacing of 0.
> Please use caution.
> Next I tried used Volume, and set DWI Component, but I dont see this option.
> I tried following as is described in tutorial:
> DiffusionMRIanalysis_Tutorial_SoniaPujol_2013 (all works fine if I used
> exemple date)
> Could you tell me, how can I repair my series DWI? Or maybe it is useless
> series?
> Series looks like dicom, but not DWI? Is possible to use this series to
> create tractography?
> Regards
> Krzysztof
>
> _______________________________________________
> 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
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>


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contains patient information, please contact the Partners Compliance HelpLine at
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Re: Problem with opening DWI series

O'Donnell, Lauren J., Ph.D.
In reply to this post by Andrey Fedorov-2
Hello,

Yes you should try to load using this module:
Diffusion->Diffusion Data Conversion->DWIConverter

Using the DicomToNrrd option. Other parameters are:

Input DWI File (None)
Output DWI Volume File (Pick a name for your new diffusion dataset.)
Input Dicom Data Directory (Choose the directory/folder where your DICOM scan is located)

Make sure only one DICOM scan is located in the input directory. If your acquisition has multiple DICOMS together,  make sure you copy your DWI scan into its own directory. 

Let us know if this works.

Lauren O’Donnell, Ph.D.
Assistant Professor, Harvard Medical School
http://scholar.harvard.edu/laurenjodonnell
1249 Boylston St., Room #210
Boston, Massachusetts 02215
[hidden email]

On Oct 3, 2015, at 10:09 PM, Andrey Fedorov <[hidden email]> wrote:

Hi,

it seems that your DWI dataset is being loaded as a scalar volume.
This will NOT work, it must be loaded as DWI.

I do not work with DWI and don't know the current and recommended
process (I would hope that the tutorial you are following should have
it described, but I just don't know, and it doesn't sound like it
does). You may want to look into using DWConvert on your data first,
but, again, I do not know whether Slicer has the proper version of
DWConvert.

If you follow the proper process, you may be able to load this
dataset, but I defer to the DWI experts to describe what the proper
process is.

AF

On Sat, Oct 3, 2015 at 2:57 PM, Krzysztof Grandys
<[hidden email]> wrote:
I tried create tractography like tutorial. I have series of dicom
https://www.dropbox.com/s/vhidw6qlws8o14m/anonym.zip?dl=0
It was named DWI AX ....
Openig series is with errors:
Images are not equally spaced (a difference of 6.00002 in spacings was
detected).  Slicer will load this series as if it had a spacing of 0.
Please use caution.
Next I tried used Volume, and set DWI Component, but I dont see this option.
I tried following as is described in tutorial:
DiffusionMRIanalysis_Tutorial_SoniaPujol_2013 (all works fine if I used
exemple date)
Could you tell me, how can I repair my series DWI? Or maybe it is useless
series?
Series looks like dicom, but not DWI? Is possible to use this series to
create tractography?
Regards
Krzysztof

_______________________________________________
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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in
error
but does not contain patient information, please contact the sender and
properly
dispose of the e-mail.

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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Re: Problem with opening DWI series

krzys59
In reply to this post by Andrey Fedorov-2
Thanks
Works fine, create DWI, but I have still problem with my dicom series. I suppose this is problem with my series not with slicer.
I tried all series, step by step, created DWI without of error, but when I tried open it, I have only 1 DWI component in Volume modul, and still can`t create tractography.
Could you look at my series and try create DWI from it? Maybe there is a solution?
Regards
Krzysztof

2015-10-04 14:14 GMT+02:00 O'Donnell, Lauren J., Ph.D. <[hidden email]>:
Hello,

Yes you should try to load using this module:
Diffusion->Diffusion Data Conversion->DWIConverter

Using the DicomToNrrd option. Other parameters are:

Input DWI File (None)
Output DWI Volume File (Pick a name for your new diffusion dataset.)
Input Dicom Data Directory (Choose the directory/folder where your DICOM scan is located)

Make sure only one DICOM scan is located in the input directory. If your acquisition has multiple DICOMS together,  make sure you copy your DWI scan into its own directory. 

Let us know if this works.

Lauren O’Donnell, Ph.D.
Assistant Professor, Harvard Medical School
http://scholar.harvard.edu/laurenjodonnell
1249 Boylston St., Room #210
Boston, Massachusetts 02215
[hidden email]

On Oct 3, 2015, at 10:09 PM, Andrey Fedorov <[hidden email]> wrote:

Hi,

it seems that your DWI dataset is being loaded as a scalar volume.
This will NOT work, it must be loaded as DWI.

I do not work with DWI and don't know the current and recommended
process (I would hope that the tutorial you are following should have
it described, but I just don't know, and it doesn't sound like it
does). You may want to look into using DWConvert on your data first,
but, again, I do not know whether Slicer has the proper version of
DWConvert.

If you follow the proper process, you may be able to load this
dataset, but I defer to the DWI experts to describe what the proper
process is.

AF

On Sat, Oct 3, 2015 at 2:57 PM, Krzysztof Grandys
<[hidden email]> wrote:
I tried create tractography like tutorial. I have series of dicom
https://www.dropbox.com/s/vhidw6qlws8o14m/anonym.zip?dl=0
It was named DWI AX ....
Openig series is with errors:
Images are not equally spaced (a difference of 6.00002 in spacings was
detected).  Slicer will load this series as if it had a spacing of 0.
Please use caution.
Next I tried used Volume, and set DWI Component, but I dont see this option.
I tried following as is described in tutorial:
DiffusionMRIanalysis_Tutorial_SoniaPujol_2013 (all works fine if I used
exemple date)
Could you tell me, how can I repair my series DWI? Or maybe it is useless
series?
Series looks like dicom, but not DWI? Is possible to use this series to
create tractography?
Regards
Krzysztof

_______________________________________________
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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in
error
but does not contain patient information, please contact the sender and
properly
dispose of the e-mail.

_______________________________________________
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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Re: Problem with opening DWI series

O'Donnell, Lauren J., Ph.D.
In reply to this post by Andrey Fedorov-2
Hello. I could not download your dataset to test--the dropbox link does not work.  

Lauren

Sent from my iPhone

On Oct 4, 2015, at 10:47 PM, Krzysztof Grandys <[hidden email]> wrote:

Thanks
Works fine, create DWI, but I have still problem with my dicom series. I suppose this is problem with my series not with slicer.
I tried all series, step by step, created DWI without of error, but when I tried open it, I have only 1 DWI component in Volume modul, and still can`t create tractography.
Could you look at my series and try create DWI from it? Maybe there is a solution?
Regards
Krzysztof

2015-10-04 14:14 GMT+02:00 O'Donnell, Lauren J., Ph.D. <[hidden email]>:
Hello,

Yes you should try to load using this module:
Diffusion->Diffusion Data Conversion->DWIConverter

Using the DicomToNrrd option. Other parameters are:

Input DWI File (None)
Output DWI Volume File (Pick a name for your new diffusion dataset.)
Input Dicom Data Directory (Choose the directory/folder where your DICOM scan is located)

Make sure only one DICOM scan is located in the input directory. If your acquisition has multiple DICOMS together,  make sure you copy your DWI scan into its own directory. 

Let us know if this works.

Lauren O’Donnell, Ph.D.
Assistant Professor, Harvard Medical School
http://scholar.harvard.edu/laurenjodonnell
1249 Boylston St., Room #210
Boston, Massachusetts 02215
[hidden email]

On Oct 3, 2015, at 10:09 PM, Andrey Fedorov <[hidden email]> wrote:

Hi,

it seems that your DWI dataset is being loaded as a scalar volume.
This will NOT work, it must be loaded as DWI.

I do not work with DWI and don't know the current and recommended
process (I would hope that the tutorial you are following should have
it described, but I just don't know, and it doesn't sound like it
does). You may want to look into using DWConvert on your data first,
but, again, I do not know whether Slicer has the proper version of
DWConvert.

If you follow the proper process, you may be able to load this
dataset, but I defer to the DWI experts to describe what the proper
process is.

AF

On Sat, Oct 3, 2015 at 2:57 PM, Krzysztof Grandys
<[hidden email]> wrote:
I tried create tractography like tutorial. I have series of dicom
https://www.dropbox.com/s/vhidw6qlws8o14m/anonym.zip?dl=0
It was named DWI AX ....
Openig series is with errors:
Images are not equally spaced (a difference of 6.00002 in spacings was
detected).  Slicer will load this series as if it had a spacing of 0.
Please use caution.
Next I tried used Volume, and set DWI Component, but I dont see this option.
I tried following as is described in tutorial:
DiffusionMRIanalysis_Tutorial_SoniaPujol_2013 (all works fine if I used
exemple date)
Could you tell me, how can I repair my series DWI? Or maybe it is useless
series?
Series looks like dicom, but not DWI? Is possible to use this series to
create tractography?
Regards
Krzysztof

_______________________________________________
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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in
error
but does not contain patient information, please contact the sender and
properly
dispose of the e-mail.

_______________________________________________
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: Problem with opening DWI series

krzys59
In reply to this post by Andrey Fedorov-2

2015-10-04 22:51 GMT+02:00 O'Donnell, Lauren J., Ph.D. <[hidden email]>:
Hello. I could not download your dataset to test--the dropbox link does not work.  

Lauren

Sent from my iPhone

On Oct 4, 2015, at 10:47 PM, Krzysztof Grandys <[hidden email]> wrote:

Thanks
Works fine, create DWI, but I have still problem with my dicom series. I suppose this is problem with my series not with slicer.
I tried all series, step by step, created DWI without of error, but when I tried open it, I have only 1 DWI component in Volume modul, and still can`t create tractography.
Could you look at my series and try create DWI from it? Maybe there is a solution?
Regards
Krzysztof

2015-10-04 14:14 GMT+02:00 O'Donnell, Lauren J., Ph.D. <[hidden email]>:
Hello,

Yes you should try to load using this module:
Diffusion->Diffusion Data Conversion->DWIConverter

Using the DicomToNrrd option. Other parameters are:

Input DWI File (None)
Output DWI Volume File (Pick a name for your new diffusion dataset.)
Input Dicom Data Directory (Choose the directory/folder where your DICOM scan is located)

Make sure only one DICOM scan is located in the input directory. If your acquisition has multiple DICOMS together,  make sure you copy your DWI scan into its own directory. 

Let us know if this works.

Lauren O’Donnell, Ph.D.
Assistant Professor, Harvard Medical School
http://scholar.harvard.edu/laurenjodonnell
1249 Boylston St., Room #210
Boston, Massachusetts 02215
[hidden email]

On Oct 3, 2015, at 10:09 PM, Andrey Fedorov <[hidden email]> wrote:

Hi,

it seems that your DWI dataset is being loaded as a scalar volume.
This will NOT work, it must be loaded as DWI.

I do not work with DWI and don't know the current and recommended
process (I would hope that the tutorial you are following should have
it described, but I just don't know, and it doesn't sound like it
does). You may want to look into using DWConvert on your data first,
but, again, I do not know whether Slicer has the proper version of
DWConvert.

If you follow the proper process, you may be able to load this
dataset, but I defer to the DWI experts to describe what the proper
process is.

AF

On Sat, Oct 3, 2015 at 2:57 PM, Krzysztof Grandys
<[hidden email]> wrote:
I tried create tractography like tutorial. I have series of dicom
https://www.dropbox.com/s/vhidw6qlws8o14m/anonym.zip?dl=0
It was named DWI AX ....
Openig series is with errors:
Images are not equally spaced (a difference of 6.00002 in spacings was
detected).  Slicer will load this series as if it had a spacing of 0.
Please use caution.
Next I tried used Volume, and set DWI Component, but I dont see this option.
I tried following as is described in tutorial:
DiffusionMRIanalysis_Tutorial_SoniaPujol_2013 (all works fine if I used
exemple date)
Could you tell me, how can I repair my series DWI? Or maybe it is useless
series?
Series looks like dicom, but not DWI? Is possible to use this series to
create tractography?
Regards
Krzysztof

_______________________________________________
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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in
error
but does not contain patient information, please contact the sender and
properly
dispose of the e-mail.

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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Re: Problem with opening DWI series

O'Donnell, Lauren J., Ph.D.
In reply to this post by Andrey Fedorov-2
Unfortunately I am unable to load this dataset into a recent Slicer nightly either as standard DICOM or in the DWIConvert module. Is this the same dataset that you were able to load in your Slicer?

Lauren

On Oct 5, 2015, at 8:30 AM, Krzysztof Grandys <[hidden email]> wrote:


2015-10-04 22:51 GMT+02:00 O'Donnell, Lauren J., Ph.D. <[hidden email]>:
Hello. I could not download your dataset to test--the dropbox link does not work.  

Lauren

Sent from my iPhone

On Oct 4, 2015, at 10:47 PM, Krzysztof Grandys <[hidden email]> wrote:

Thanks
Works fine, create DWI, but I have still problem with my dicom series. I suppose this is problem with my series not with slicer.
I tried all series, step by step, created DWI without of error, but when I tried open it, I have only 1 DWI component in Volume modul, and still can`t create tractography.
Could you look at my series and try create DWI from it? Maybe there is a solution?
Regards
Krzysztof

2015-10-04 14:14 GMT+02:00 O'Donnell, Lauren J., Ph.D. <[hidden email]>:
Hello,

Yes you should try to load using this module:
Diffusion->Diffusion Data Conversion->DWIConverter

Using the DicomToNrrd option. Other parameters are:

Input DWI File (None)
Output DWI Volume File (Pick a name for your new diffusion dataset.)
Input Dicom Data Directory (Choose the directory/folder where your DICOM scan is located)

Make sure only one DICOM scan is located in the input directory. If your acquisition has multiple DICOMS together,  make sure you copy your DWI scan into its own directory. 

Let us know if this works.

Lauren O’Donnell, Ph.D.
Assistant Professor, Harvard Medical School
http://scholar.harvard.edu/laurenjodonnell
1249 Boylston St., Room #210
Boston, Massachusetts 02215
[hidden email]

On Oct 3, 2015, at 10:09 PM, Andrey Fedorov <[hidden email]> wrote:

Hi,

it seems that your DWI dataset is being loaded as a scalar volume.
This will NOT work, it must be loaded as DWI.

I do not work with DWI and don't know the current and recommended
process (I would hope that the tutorial you are following should have
it described, but I just don't know, and it doesn't sound like it
does). You may want to look into using DWConvert on your data first,
but, again, I do not know whether Slicer has the proper version of
DWConvert.

If you follow the proper process, you may be able to load this
dataset, but I defer to the DWI experts to describe what the proper
process is.

AF

On Sat, Oct 3, 2015 at 2:57 PM, Krzysztof Grandys
<[hidden email]> wrote:
I tried create tractography like tutorial. I have series of dicom
https://www.dropbox.com/s/vhidw6qlws8o14m/anonym.zip?dl=0
It was named DWI AX ....
Openig series is with errors:
Images are not equally spaced (a difference of 6.00002 in spacings was
detected).  Slicer will load this series as if it had a spacing of 0.
Please use caution.
Next I tried used Volume, and set DWI Component, but I dont see this option.
I tried following as is described in tutorial:
DiffusionMRIanalysis_Tutorial_SoniaPujol_2013 (all works fine if I used
exemple date)
Could you tell me, how can I repair my series DWI? Or maybe it is useless
series?
Series looks like dicom, but not DWI? Is possible to use this series to
create tractography?
Regards
Krzysztof

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
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unsubscribe as the subject
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contains patient information, please contact the Partners Compliance
HelpLine at
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Re: Problem with opening DWI series

O'Donnell, Lauren J., Ph.D.
In reply to this post by Andrey Fedorov-2
Hi again Krzysztof,

When I load your new scan in DWIConvert, I get only two components, where one looks to be diffusion-weighted and the second to have a diffusion weighting near 0. The DICOM says it is a DWI scan, but I do not see evidence that it is a diffusion tensor scan, which would require more diffusion weighted images (usually 20 or more). Also, the total size of the scan is quite small (9.6M), so it does not seem possible that it is a DTI scan.

For tractography, you should acquire about 20 gradient directions for a DTI scan, or more directions (30-60) for a HARDI-style scan.

I hope this helps.

Lauren O’Donnell, Ph.D.
Assistant Professor, Harvard Medical School
http://scholar.harvard.edu/laurenjodonnell
1249 Boylston St., Room #210
Boston, Massachusetts 02215
[hidden email]

On Oct 5, 2015, at 11:14 AM, Lauren O'Donnell <[hidden email]> wrote:

Unfortunately I am unable to load this dataset into a recent Slicer nightly either as standard DICOM or in the DWIConvert module. Is this the same dataset that you were able to load in your Slicer?

Lauren

On Oct 5, 2015, at 8:30 AM, Krzysztof Grandys <[hidden email]> wrote:


2015-10-04 22:51 GMT+02:00 O'Donnell, Lauren J., Ph.D. <[hidden email]>:
Hello. I could not download your dataset to test--the dropbox link does not work.  

Lauren

Sent from my iPhone

On Oct 4, 2015, at 10:47 PM, Krzysztof Grandys <[hidden email]> wrote:

Thanks
Works fine, create DWI, but I have still problem with my dicom series. I suppose this is problem with my series not with slicer.
I tried all series, step by step, created DWI without of error, but when I tried open it, I have only 1 DWI component in Volume modul, and still can`t create tractography.
Could you look at my series and try create DWI from it? Maybe there is a solution?
Regards
Krzysztof

2015-10-04 14:14 GMT+02:00 O'Donnell, Lauren J., Ph.D. <[hidden email]>:
Hello,

Yes you should try to load using this module:
Diffusion->Diffusion Data Conversion->DWIConverter

Using the DicomToNrrd option. Other parameters are:

Input DWI File (None)
Output DWI Volume File (Pick a name for your new diffusion dataset.)
Input Dicom Data Directory (Choose the directory/folder where your DICOM scan is located)

Make sure only one DICOM scan is located in the input directory. If your acquisition has multiple DICOMS together,  make sure you copy your DWI scan into its own directory. 

Let us know if this works.

Lauren O’Donnell, Ph.D.
Assistant Professor, Harvard Medical School
http://scholar.harvard.edu/laurenjodonnell
1249 Boylston St., Room #210
Boston, Massachusetts 02215
[hidden email]

On Oct 3, 2015, at 10:09 PM, Andrey Fedorov <[hidden email]> wrote:

Hi,

it seems that your DWI dataset is being loaded as a scalar volume.
This will NOT work, it must be loaded as DWI.

I do not work with DWI and don't know the current and recommended
process (I would hope that the tutorial you are following should have
it described, but I just don't know, and it doesn't sound like it
does). You may want to look into using DWConvert on your data first,
but, again, I do not know whether Slicer has the proper version of
DWConvert.

If you follow the proper process, you may be able to load this
dataset, but I defer to the DWI experts to describe what the proper
process is.

AF

On Sat, Oct 3, 2015 at 2:57 PM, Krzysztof Grandys
<[hidden email]> wrote:
I tried create tractography like tutorial. I have series of dicom
https://www.dropbox.com/s/vhidw6qlws8o14m/anonym.zip?dl=0
It was named DWI AX ....
Openig series is with errors:
Images are not equally spaced (a difference of 6.00002 in spacings was
detected).  Slicer will load this series as if it had a spacing of 0.
Please use caution.
Next I tried used Volume, and set DWI Component, but I dont see this option.
I tried following as is described in tutorial:
DiffusionMRIanalysis_Tutorial_SoniaPujol_2013 (all works fine if I used
exemple date)
Could you tell me, how can I repair my series DWI? Or maybe it is useless
series?
Series looks like dicom, but not DWI? Is possible to use this series to
create tractography?
Regards
Krzysztof

_______________________________________________
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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in
error
but does not contain patient information, please contact the sender and
properly
dispose of the e-mail.

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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Re: Problem with opening DWI series

Andrey Fedorov-2
In reply to this post by Andrey Fedorov-2
It is my experience in prostate imaging that a DWI series can save
just the trace, and only few (in our case, 3) directions are used.
Such sequences are not intended for DTI analysis. In the prostate we
use them only for quantification of ADC and other parameters using
diffusion models.

On Mon, Oct 5, 2015 at 9:00 AM, O'Donnell, Lauren J., Ph.D.
<[hidden email]> wrote:

> Hi again Krzysztof,
>
> When I load your new scan in DWIConvert, I get only two components, where
> one looks to be diffusion-weighted and the second to have a diffusion
> weighting near 0. The DICOM says it is a DWI scan, but I do not see evidence
> that it is a diffusion tensor scan, which would require more diffusion
> weighted images (usually 20 or more). Also, the total size of the scan is
> quite small (9.6M), so it does not seem possible that it is a DTI scan.
>
> For tractography, you should acquire about 20 gradient directions for a DTI
> scan, or more directions (30-60) for a HARDI-style scan.
>
> I hope this helps.
>
> Lauren O’Donnell, Ph.D.
> Assistant Professor, Harvard Medical School
> http://scholar.harvard.edu/laurenjodonnell
> 1249 Boylston St., Room #210
> Boston, Massachusetts 02215
> [hidden email]
>
> On Oct 5, 2015, at 11:14 AM, Lauren O'Donnell <[hidden email]>
> wrote:
>
> Unfortunately I am unable to load this dataset into a recent Slicer nightly
> either as standard DICOM or in the DWIConvert module. Is this the same
> dataset that you were able to load in your Slicer?
>
> Lauren
>
> On Oct 5, 2015, at 8:30 AM, Krzysztof Grandys <[hidden email]>
> wrote:
>
> https://www.dropbox.com/s/bb65pj5etfk53mc/Anonymous_MRI.zip?dl=0
> I thing this link is correct
> Krzysztof
>
> 2015-10-04 22:51 GMT+02:00 O'Donnell, Lauren J., Ph.D.
> <[hidden email]>:
>>
>> Hello. I could not download your dataset to test--the dropbox link does
>> not work.
>>
>> Lauren
>>
>> Sent from my iPhone
>>
>> On Oct 4, 2015, at 10:47 PM, Krzysztof Grandys <[hidden email]>
>> wrote:
>>
>> Thanks
>> Works fine, create DWI, but I have still problem with my dicom series. I
>> suppose this is problem with my series not with slicer.
>> I tried all series, step by step, created DWI without of error, but when I
>> tried open it, I have only 1 DWI component in Volume modul, and still can`t
>> create tractography.
>> Could you look at my series and try create DWI from it? Maybe there is a
>> solution?
>> Regards
>> Krzysztof
>>
>> 2015-10-04 14:14 GMT+02:00 O'Donnell, Lauren J., Ph.D.
>> <[hidden email]>:
>>>
>>> Hello,
>>>
>>> Yes you should try to load using this module:
>>> Diffusion->Diffusion Data Conversion->DWIConverter
>>>
>>> Using the DicomToNrrd option. Other parameters are:
>>>
>>> Input DWI File (None)
>>> Output DWI Volume File (Pick a name for your new diffusion dataset.)
>>> Input Dicom Data Directory (Choose the directory/folder where your DICOM
>>> scan is located)
>>>
>>> Make sure only one DICOM scan is located in the input directory. If your
>>> acquisition has multiple DICOMS together,  make sure you copy your DWI scan
>>> into its own directory.
>>>
>>> Let us know if this works.
>>>
>>> Lauren O’Donnell, Ph.D.
>>> Assistant Professor, Harvard Medical School
>>> http://scholar.harvard.edu/laurenjodonnell
>>> 1249 Boylston St., Room #210
>>> Boston, Massachusetts 02215
>>> [hidden email]
>>>
>>> On Oct 3, 2015, at 10:09 PM, Andrey Fedorov <[hidden email]>
>>> wrote:
>>>
>>> Hi,
>>>
>>> it seems that your DWI dataset is being loaded as a scalar volume.
>>> This will NOT work, it must be loaded as DWI.
>>>
>>> I do not work with DWI and don't know the current and recommended
>>> process (I would hope that the tutorial you are following should have
>>> it described, but I just don't know, and it doesn't sound like it
>>> does). You may want to look into using DWConvert on your data first,
>>> but, again, I do not know whether Slicer has the proper version of
>>> DWConvert.
>>>
>>> If you follow the proper process, you may be able to load this
>>> dataset, but I defer to the DWI experts to describe what the proper
>>> process is.
>>>
>>> AF
>>>
>>> On Sat, Oct 3, 2015 at 2:57 PM, Krzysztof Grandys
>>> <[hidden email]> wrote:
>>>
>>> I tried create tractography like tutorial. I have series of dicom
>>> https://www.dropbox.com/s/vhidw6qlws8o14m/anonym.zip?dl=0
>>> It was named DWI AX ....
>>> Openig series is with errors:
>>> Images are not equally spaced (a difference of 6.00002 in spacings was
>>> detected).  Slicer will load this series as if it had a spacing of 0.
>>> Please use caution.
>>> Next I tried used Volume, and set DWI Component, but I dont see this
>>> option.
>>> I tried following as is described in tutorial:
>>> DiffusionMRIanalysis_Tutorial_SoniaPujol_2013 (all works fine if I used
>>> exemple date)
>>> Could you tell me, how can I repair my series DWI? Or maybe it is useless
>>> series?
>>> Series looks like dicom, but not DWI? Is possible to use this series to
>>> create tractography?
>>> Regards
>>> Krzysztof
>>>
>>> _______________________________________________
>>> 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
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom it
>>> is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you in
>>> error
>>> but does not contain patient information, please contact the sender and
>>> properly
>>> dispose of the e-mail.
>>>
>>> _______________________________________________
>>> 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
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Re: Problem with opening DWI series

Min Pu
Dear all

I combine two stl files. I want to learn how to direct 3D printer to print in different color or material on dual extruder printers.

Thanks

Min Pu, MD, PhD
Wake Forest University School of Medicine
Baptist Medical Center
Tel: 336-716-9862
Fax: 336-716-4995

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Andrey Fedorov
Sent: Monday, October 05, 2015 9:12 AM
To: O'Donnell, Lauren J., Ph.D.
Cc: SPL Slicer Users; Krzysztof Grandys
Subject: Re: [slicer-users] Problem with opening DWI series

It is my experience in prostate imaging that a DWI series can save just the trace, and only few (in our case, 3) directions are used.
Such sequences are not intended for DTI analysis. In the prostate we use them only for quantification of ADC and other parameters using diffusion models.

On Mon, Oct 5, 2015 at 9:00 AM, O'Donnell, Lauren J., Ph.D.
<[hidden email]> wrote:

> Hi again Krzysztof,
>
> When I load your new scan in DWIConvert, I get only two components,
> where one looks to be diffusion-weighted and the second to have a
> diffusion weighting near 0. The DICOM says it is a DWI scan, but I do
> not see evidence that it is a diffusion tensor scan, which would
> require more diffusion weighted images (usually 20 or more). Also, the
> total size of the scan is quite small (9.6M), so it does not seem possible that it is a DTI scan.
>
> For tractography, you should acquire about 20 gradient directions for
> a DTI scan, or more directions (30-60) for a HARDI-style scan.
>
> I hope this helps.
>
> Lauren O'Donnell, Ph.D.
> Assistant Professor, Harvard Medical School
> http://scholar.harvard.edu/laurenjodonnell
> 1249 Boylston St., Room #210
> Boston, Massachusetts 02215
> [hidden email]
>
> On Oct 5, 2015, at 11:14 AM, Lauren O'Donnell
> <[hidden email]>
> wrote:
>
> Unfortunately I am unable to load this dataset into a recent Slicer
> nightly either as standard DICOM or in the DWIConvert module. Is this
> the same dataset that you were able to load in your Slicer?
>
> Lauren
>
> On Oct 5, 2015, at 8:30 AM, Krzysztof Grandys <[hidden email]>
> wrote:
>
> https://www.dropbox.com/s/bb65pj5etfk53mc/Anonymous_MRI.zip?dl=0
> I thing this link is correct
> Krzysztof
>
> 2015-10-04 22:51 GMT+02:00 O'Donnell, Lauren J., Ph.D.
> <[hidden email]>:
>>
>> Hello. I could not download your dataset to test--the dropbox link
>> does not work.
>>
>> Lauren
>>
>> Sent from my iPhone
>>
>> On Oct 4, 2015, at 10:47 PM, Krzysztof Grandys
>> <[hidden email]>
>> wrote:
>>
>> Thanks
>> Works fine, create DWI, but I have still problem with my dicom
>> series. I suppose this is problem with my series not with slicer.
>> I tried all series, step by step, created DWI without of error, but
>> when I tried open it, I have only 1 DWI component in Volume modul,
>> and still can`t create tractography.
>> Could you look at my series and try create DWI from it? Maybe there
>> is a solution?
>> Regards
>> Krzysztof
>>
>> 2015-10-04 14:14 GMT+02:00 O'Donnell, Lauren J., Ph.D.
>> <[hidden email]>:
>>>
>>> Hello,
>>>
>>> Yes you should try to load using this module:
>>> Diffusion->Diffusion Data Conversion->DWIConverter
>>>
>>> Using the DicomToNrrd option. Other parameters are:
>>>
>>> Input DWI File (None)
>>> Output DWI Volume File (Pick a name for your new diffusion dataset.)
>>> Input Dicom Data Directory (Choose the directory/folder where your
>>> DICOM scan is located)
>>>
>>> Make sure only one DICOM scan is located in the input directory. If
>>> your acquisition has multiple DICOMS together,  make sure you copy
>>> your DWI scan into its own directory.
>>>
>>> Let us know if this works.
>>>
>>> Lauren O'Donnell, Ph.D.
>>> Assistant Professor, Harvard Medical School
>>> http://scholar.harvard.edu/laurenjodonnell
>>> 1249 Boylston St., Room #210
>>> Boston, Massachusetts 02215
>>> [hidden email]
>>>
>>> On Oct 3, 2015, at 10:09 PM, Andrey Fedorov
>>> <[hidden email]>
>>> wrote:
>>>
>>> Hi,
>>>
>>> it seems that your DWI dataset is being loaded as a scalar volume.
>>> This will NOT work, it must be loaded as DWI.
>>>
>>> I do not work with DWI and don't know the current and recommended
>>> process (I would hope that the tutorial you are following should
>>> have it described, but I just don't know, and it doesn't sound like
>>> it does). You may want to look into using DWConvert on your data
>>> first, but, again, I do not know whether Slicer has the proper
>>> version of DWConvert.
>>>
>>> If you follow the proper process, you may be able to load this
>>> dataset, but I defer to the DWI experts to describe what the proper
>>> process is.
>>>
>>> AF
>>>
>>> On Sat, Oct 3, 2015 at 2:57 PM, Krzysztof Grandys
>>> <[hidden email]> wrote:
>>>
>>> I tried create tractography like tutorial. I have series of dicom
>>> https://www.dropbox.com/s/vhidw6qlws8o14m/anonym.zip?dl=0
>>> It was named DWI AX ....
>>> Openig series is with errors:
>>> Images are not equally spaced (a difference of 6.00002 in spacings
>>> was detected).  Slicer will load this series as if it had a spacing of 0.
>>> Please use caution.
>>> Next I tried used Volume, and set DWI Component, but I dont see this
>>> option.
>>> I tried following as is described in tutorial:
>>> DiffusionMRIanalysis_Tutorial_SoniaPujol_2013 (all works fine if I
>>> used exemple date) Could you tell me, how can I repair my series
>>> DWI? Or maybe it is useless series?
>>> Series looks like dicom, but not DWI? Is possible to use this series
>>> to create tractography?
>>> Regards
>>> Krzysztof
>>>
>>> _______________________________________________
>>> 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
>>>
>>>
>>> The information in this e-mail is intended only for the person to
>>> whom it is addressed. If you believe this e-mail was sent to you in
>>> error and the e-mail contains patient information, please contact
>>> the Partners Compliance HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to
>>> you in error but does not contain patient information, please
>>> contact the sender and properly dispose of the e-mail.
>>>
>>> _______________________________________________
>>> 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

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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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Re: Problem with opening DWI series

O'Donnell, Lauren J., Ph.D.
In reply to this post by Andrey Fedorov-2
Hi again Krzysztof:

It looks like this DICOM format is not what Slicer’s DWIConvert is expecting, or what the DICOM module is expecting, since I can’t load any of your DICOM data with the nightly Slicer. 

I am cc’ing the developer list because this is beyond my experience with DICOM loading. 

I tried your latest dataset in DWIConvert. However this DWI is only 5.8 MB and one component so it can’t really be a DTI scan. I also tried the one in 0012 since it’s larger but I got the same errors.

Then I tried loading several of your datasets in the standard DICOM module and it tries to load it as a MultiVolume but the resulting image is a white square. For the DWI dataset, the message it gives is: Loaded volume from file: /Users/lauren/Downloads/STU0001/SER0007/IMG0001. Dimensions: 256x256x25. Number of components: 1. Pixel type: short.

Lauren

Here’s the DWIConverter error (same for both datasets I tried).
DWIConverter standard error:

E: can't change to unencapsulated representation for pixel data
E: can't determine 'PhotometricInterpretation' of decompressed image
E: mandatory attribute 'PhotometricInterpretation' is missing or can't be determined
E: can't change to unencapsulated representation for pixel data
E: can't determine 'PhotometricInterpretation' of decompressed image
E: mandatory attribute 'PhotometricInterpretation' is missing or can't be determined
E: can't change to unencapsulated representation for pixel data
E: can't determine 'PhotometricInterpretation' of decompressed image
E: mandatory attribute 'PhotometricInterpretation' is missing or can't be determined
E: can't change to unencapsulated representation for pixel data
E: can't determine 'PhotometricInterpretation' of decompressed image
E: mandatory attribute 'PhotometricInterpretation' is missing or can't be determined
E: can't change to unencapsulated representation for pixel data
E: can't determine 'PhotometricInterpretation' of decompressed image
E: mandatory attribute 'PhotometricInterpretation' is missing or can't be determined
E: can't change to unencapsulated representation for pixel data
E: can't determine 'PhotometricInterpretation' of decompressed image
E: mandatory attribute 'PhotometricInterpretation' is missing or can't be determined
E: can't change to unencapsulated representation for pixel data
E: can't determine 'PhotometricInterpretation' of decompressed image
E: mandatory attribute 'PhotometricInterpretation' is missing or can't be determined
E: can't change to unencapsulated representation for pixel data
E: can't determine 'PhotometricInterpretation' of decompressed image
E: mandatory attribute 'PhotometricInterpretation' is missing or can't be determined
E: can't change to unencapsulated representation for pixel data
E: can't determine 'PhotometricInterpretation' of decompressed image
E: mandatory attribute 'PhotometricInterpretation' is missing or can't be determined
E: can't change to unencapsulated representation for pixel data
E: can't determine 'PhotometricInterpretation' of decompressed image
E: mandatory attribute 'PhotometricInterpretation' is missing or can't be determined
E: can't change to unencapsulated representation for pixel data
E: can't determine 'PhotometricInterpretation' of decompressed image
E: mandatory attribute 'PhotometricInterpretation' is missing or can't be determined
E: can't change to unencapsulated representation for pixel data
E: can't determine 'PhotometricInterpretation' of decompressed image
E: mandatory attribute 'PhotometricInterpretation' is missing or can't be determined
E: can't change to unencapsulated representation for pixel data
E: can't determine 'PhotometricInterpretation' of decompressed image
E: mandatory attribute 'PhotometricInterpretation' is missing or can't be determined
E: can't change to unencapsulated representation for pixel data
E: can't determine 'PhotometricInterpretation' of decompressed image
E: mandatory attribute 'PhotometricInterpretation' is missing or can't be determined
E: can't change to unencapsulated representation for pixel data
E: can't determine 'PhotometricInterpretation' of decompressed image
E: mandatory attribute 'PhotometricInterpretation' is missing or can't be determined
E: can't change to unencapsulated representation for pixel data
E: can't determine 'PhotometricInterpretation' of decompressed image
E: mandatory attribute 'PhotometricInterpretation' is missing or can't be determined
E: can't change to unencapsulated representation for pixel data
E: can't determine 'PhotometricInterpretation' of decompressed image
E: mandatory attribute 'PhotometricInterpretation' is missing or can't be determined
E: can't change to unencapsulated representation for pixel data
E: can't determine 'PhotometricInterpretation' of decompressed image
E: mandatory attribute 'PhotometricInterpretation' is missing or can't be determined
E: can't change to unencapsulated representation for pixel data
E: can't determine 'PhotometricInterpretation' of decompressed image
E: mandatory attribute 'PhotometricInterpretation' is missing or can't be determined
E: can't change to unencapsulated representation for pixel data
E: can't determine 'PhotometricInterpretation' of decompressed image
E: mandatory attribute 'PhotometricInterpretation' is missing or can't be determined
E: can't change to unencapsulated representation for pixel data
E: can't determine 'PhotometricInterpretation' of decompressed image
E: mandatory attribute 'PhotometricInterpretation' is missing or can't be determined
E: can't change to unencapsulated representation for pixel data
E: can't determine 'PhotometricInterpretation' of decompressed image
E: mandatory attribute 'PhotometricInterpretation' is missing or can't be determined
Error: no DICOMfiles found in inputDirectory: /Users/lauren/Downloads/STU0001/SER0008



DWIConverter terminated with a fault.




Lauren O’Donnell, Ph.D.
Assistant Professor, Harvard Medical School
http://scholar.harvard.edu/laurenjodonnell
1249 Boylston St., Room #210
Boston, Massachusetts 02215
[hidden email]

On Oct 5, 2015, at 7:35 PM, Krzysztof Grandys <[hidden email]> wrote:

I do not want to abuse the patience, but could you look at this DICOM series? It is bigger than previous, and in description (polish language) looks like diffusion scans. But, I can convert anyone do DWI/ Could you try do that?
Sorry about hassle :-)
Link:
Krzysztof

2015-10-05 19:20 GMT+02:00 O'Donnell, Lauren J., Ph.D. <[hidden email]>:
You're welcome!
Lauren

Sent from my iPhone

On Oct 5, 2015, at 7:16 PM, Krzysztof Grandys <[hidden email]> wrote:

Thank you at your answer.
You give my very usefull knowlege in short form :-)
Thank you
Krzysztof

2015-10-05 15:00 GMT+02:00 O'Donnell, Lauren J., Ph.D. <[hidden email]>:
Hi again Krzysztof,

When I load your new scan in DWIConvert, I get only two components, where one looks to be diffusion-weighted and the second to have a diffusion weighting near 0. The DICOM says it is a DWI scan, but I do not see evidence that it is a diffusion tensor scan, which would require more diffusion weighted images (usually 20 or more). Also, the total size of the scan is quite small (9.6M), so it does not seem possible that it is a DTI scan.

For tractography, you should acquire about 20 gradient directions for a DTI scan, or more directions (30-60) for a HARDI-style scan.

I hope this helps.

Lauren O’Donnell, Ph.D.
Assistant Professor, Harvard Medical School
http://scholar.harvard.edu/laurenjodonnell
1249 Boylston St., Room #210
Boston, Massachusetts 02215
[hidden email]

On Oct 5, 2015, at 11:14 AM, Lauren O'Donnell <[hidden email]> wrote:

Unfortunately I am unable to load this dataset into a recent Slicer nightly either as standard DICOM or in the DWIConvert module. Is this the same dataset that you were able to load in your Slicer?

Lauren

On Oct 5, 2015, at 8:30 AM, Krzysztof Grandys <[hidden email]> wrote:


2015-10-04 22:51 GMT+02:00 O'Donnell, Lauren J., Ph.D. <[hidden email]>:
Hello. I could not download your dataset to test--the dropbox link does not work.  

Lauren

Sent from my iPhone

On Oct 4, 2015, at 10:47 PM, Krzysztof Grandys <[hidden email]> wrote:

Thanks
Works fine, create DWI, but I have still problem with my dicom series. I suppose this is problem with my series not with slicer.
I tried all series, step by step, created DWI without of error, but when I tried open it, I have only 1 DWI component in Volume modul, and still can`t create tractography.
Could you look at my series and try create DWI from it? Maybe there is a solution?
Regards
Krzysztof

2015-10-04 14:14 GMT+02:00 O'Donnell, Lauren J., Ph.D. <[hidden email]>:
Hello,

Yes you should try to load using this module:
Diffusion->Diffusion Data Conversion->DWIConverter

Using the DicomToNrrd option. Other parameters are:

Input DWI File (None)
Output DWI Volume File (Pick a name for your new diffusion dataset.)
Input Dicom Data Directory (Choose the directory/folder where your DICOM scan is located)

Make sure only one DICOM scan is located in the input directory. If your acquisition has multiple DICOMS together,  make sure you copy your DWI scan into its own directory. 

Let us know if this works.

Lauren O’Donnell, Ph.D.
Assistant Professor, Harvard Medical School
http://scholar.harvard.edu/laurenjodonnell
1249 Boylston St., Room #210
Boston, Massachusetts 02215
[hidden email]

On Oct 3, 2015, at 10:09 PM, Andrey Fedorov <[hidden email]> wrote:

Hi,

it seems that your DWI dataset is being loaded as a scalar volume.
This will NOT work, it must be loaded as DWI.

I do not work with DWI and don't know the current and recommended
process (I would hope that the tutorial you are following should have
it described, but I just don't know, and it doesn't sound like it
does). You may want to look into using DWConvert on your data first,
but, again, I do not know whether Slicer has the proper version of
DWConvert.

If you follow the proper process, you may be able to load this
dataset, but I defer to the DWI experts to describe what the proper
process is.

AF

On Sat, Oct 3, 2015 at 2:57 PM, Krzysztof Grandys
<[hidden email]> wrote:
I tried create tractography like tutorial. I have series of dicom
https://www.dropbox.com/s/vhidw6qlws8o14m/anonym.zip?dl=0
It was named DWI AX ....
Openig series is with errors:
Images are not equally spaced (a difference of 6.00002 in spacings was
detected).  Slicer will load this series as if it had a spacing of 0.
Please use caution.
Next I tried used Volume, and set DWI Component, but I dont see this option.
I tried following as is described in tutorial:
DiffusionMRIanalysis_Tutorial_SoniaPujol_2013 (all works fine if I used
exemple date)
Could you tell me, how can I repair my series DWI? Or maybe it is useless
series?
Series looks like dicom, but not DWI? Is possible to use this series to
create tractography?
Regards
Krzysztof

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