novice question: DTI to get Tactography

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novice question: DTI to get Tactography

Meredith Mahnke

Hi all,

 

I am trying to get Tactography of a brain we recently imaged. I am having trouble with the initial steps… I have ADC (nhdr), LOWB (nrrd), EXP (nrrd), FA (nrrd) and colorFA (dcm) images (iso_fov128_300dir). I have read the tutorial of how to get the Tactography from a DMI…but am unsure of 1)how to approach loading and defining these filies in Slicer version 4.5.0-1, 2) at what stage in the tutorial to begin after loading. Thank you!

 

Best,

Meredith


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Re: novice question: DTI to get Tactography

O'Donnell, Lauren J., Ph.D.
Dear Meredith,

From your description, it is not clear if you have loaded the correct data. For tractography, you will need diffusion-weighted images, which are usually in a scan called DWI or DTI. The file size should be much larger than the FA or ADC images. Once you load the DWI into slicer, it should be recognized by Slicer as a DWI, enabling you to calculate tensors from it, for example.

For DICOM DWI/DTI, the DWIConvert module page is here and has a link to a tutorial and test data:

All diffusion tutorials are linked from here:

If you have more questions, please let us know 1) what image(s) you loaded and how, 2) what module you tried to use and what happened, and 3) the name of the tutorial you are following.

We recommend Slicer nightly for best diffusion support (or the upcoming Slicer 4.6 release).

I hope this helps!

Lauren

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 17, 2016, at 12:26 AM, Meredith Mahnke <[hidden email]> wrote:

Hi all,
 
I am trying to get Tactography of a brain we recently imaged. I am having trouble with the initial steps… I have ADC (nhdr), LOWB (nrrd), EXP (nrrd), FA (nrrd) and colorFA (dcm) images (iso_fov128_300dir). I have read the tutorial of how to get the Tactography from a DMI…but am unsure of 1)how to approach loading and defining these filies in Slicer version 4.5.0-1, 2) at what stage in the tutorial to begin after loading. Thank you!
 
Best,
Meredith
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Re: novice question: DTI to get Tactography

inorton
In reply to this post by Meredith Mahnke
On Sun, Oct 16, 2016 at 5:26 PM, Meredith Mahnke <[hidden email]> wrote:


I am trying to get Tactography of a brain we recently imaged. I am having trouble with the initial steps… I have ADC (nhdr), LOWB (nrrd), EXP (nrrd), FA (nrrd) and colorFA (dcm) images (iso_fov128_300dir).


Images with these names are probably post-processed scalar maps created automatically by the scanner. At least on Siemens, the naming convention is usually something like "ep2d_diff_SCALAR" (e.g. "ep2d_diff_ADC"). The sequence with the shortest name -- containing no modifier -- should be the Diffusion Weighed Image (e.g. "ep2d_diff" -- again, Siemens).

 

I have read the tutorial of how to get the Tactography from a DMI…but am unsure of 1)how to approach loading and defining these filies in Slicer version 4.5.0-1, 2) at what stage in the tutorial to begin after loading. Thank you!

 

Best,

Meredith


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Re: novice question: DTI to get Tactography

Meredith Mahnke
In reply to this post by Meredith Mahnke

Hi all,

 

I am trying to get Tactography of a brain we recently imaged. I am up to the step of seeding… I have loaded the correct  dmi file. I set the parrameters the same as to tutorial  (http://wiki.slicer.org/slicerWiki/images/8/86/DiffusionMRIanalysisTutorial_Slicer4.5_SoniaPujol.pdf) but do not see the image in the index space. I am using 4.5.0-1 (4.6 extensions did not work).

From: O'Donnell, Lauren J., Ph.D. [mailto:[hidden email]]
Sent: Monday, October 17, 2016 6:02 AM
To: Meredith Mahnke <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] novice question: DTI to get Tactography

 

Dear Meredith,

 

From your description, it is not clear if you have loaded the correct data. For tractography, you will need diffusion-weighted images, which are usually in a scan called DWI or DTI. The file size should be much larger than the FA or ADC images. Once you load the DWI into slicer, it should be recognized by Slicer as a DWI, enabling you to calculate tensors from it, for example.

 

For DICOM DWI/DTI, the DWIConvert module page is here and has a link to a tutorial and test data:

 

All diffusion tutorials are linked from here:

 

If you have more questions, please let us know 1) what image(s) you loaded and how, 2) what module you tried to use and what happened, and 3) the name of the tutorial you are following.

 

We recommend Slicer nightly for best diffusion support (or the upcoming Slicer 4.6 release).

 

I hope this helps!

 

Lauren

 

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 17, 2016, at 12:26 AM, Meredith Mahnke <[hidden email]> wrote:

 

Hi all,

 

I am trying to get Tactography of a brain we recently imaged. I am having trouble with the initial steps… I have ADC (nhdr), LOWB (nrrd), EXP (nrrd), FA (nrrd) and colorFA (dcm) images (iso_fov128_300dir). I have read the tutorial of how to get the Tactography from a DMI…but am unsure of 1)how to approach loading and defining these filies in Slicer version 4.5.0-1, 2) at what stage in the tutorial to begin after loading. Thank you!

 

Best,

Meredith

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To unsubscribe: send email to 
[hidden email] with unsubscribe as the subject
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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
http://www.partners.org/complianceline . If the e-mail was sent to you in error
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Re: novice question: DTI to get Tactography

Meredith Mahnke

I answered my own question. I set the defult to sllicer 3 and the image showed

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Meredith Mahnke
Sent: Wednesday, October 19, 2016 4:14 PM
To: O'Donnell, Lauren J., Ph.D. <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] novice question: DTI to get Tactography

 

Hi all,

 

I am trying to get Tactography of a brain we recently imaged. I am up to the step of seeding… I have loaded the correct  dmi file. I set the parrameters the same as to tutorial  (http://wiki.slicer.org/slicerWiki/images/8/86/DiffusionMRIanalysisTutorial_Slicer4.5_SoniaPujol.pdf) but do not see the image in the index space. I am using 4.5.0-1 (4.6 extensions did not work).

From: O'Donnell, Lauren J., Ph.D. [[hidden email]]
Sent: Monday, October 17, 2016 6:02 AM
To: Meredith Mahnke <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] novice question: DTI to get Tactography

 

Dear Meredith,

 

From your description, it is not clear if you have loaded the correct data. For tractography, you will need diffusion-weighted images, which are usually in a scan called DWI or DTI. The file size should be much larger than the FA or ADC images. Once you load the DWI into slicer, it should be recognized by Slicer as a DWI, enabling you to calculate tensors from it, for example.

 

For DICOM DWI/DTI, the DWIConvert module page is here and has a link to a tutorial and test data:

 

All diffusion tutorials are linked from here:

 

If you have more questions, please let us know 1) what image(s) you loaded and how, 2) what module you tried to use and what happened, and 3) the name of the tutorial you are following.

 

We recommend Slicer nightly for best diffusion support (or the upcoming Slicer 4.6 release).

 

I hope this helps!

 

Lauren

 

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 17, 2016, at 12:26 AM, Meredith Mahnke <[hidden email]> wrote:

 

Hi all,

 

I am trying to get Tactography of a brain we recently imaged. I am having trouble with the initial steps… I have ADC (nhdr), LOWB (nrrd), EXP (nrrd), FA (nrrd) and colorFA (dcm) images (iso_fov128_300dir). I have read the tutorial of how to get the Tactography from a DMI…but am unsure of 1)how to approach loading and defining these filies in Slicer version 4.5.0-1, 2) at what stage in the tutorial to begin after loading. Thank you!

 

Best,

Meredith

_______________________________________________
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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