dti data dicom to nrrd/nii conversion

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dti data dicom to nrrd/nii conversion

adeelamalik
i have acquired dti data from my scanner and transferred it to my mac. now the problem is that i cant convert the DICOM data into any other file format like nrrd or nifti.

even in the display window, the data appears bizzare and sliced. i have attached a screenshot for reference.

Inline image

i have also tried mri convert, but the error displayed in mriconvert is that
"the data doesnt contain b-0 image" but i have checked the b-0 image option in my scanner.
can anyone plz guide me where i m doing wrong?

i have also uploaded the data on dropbox if anyone would like to check out the dicom files. here is the link:




thnx for help.

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Re: dti data dicom to nrrd/nii conversion

inorton
Hello,

Thanks for the example data. Unfortunately, DWIConvert does not support Toshiba data right now. I will take a look at adding in the future ([1]).

For now, I can suggest to use dcm2nii [2] which *may* convert the data: it does extract the gradients, but it also prints a number of warnings.

Best,
Isaiah


On Thu, Jul 28, 2016 at 7:00 AM, Malik Adeel <[hidden email]> wrote:
i have acquired dti data from my scanner and transferred it to my mac. now the problem is that i cant convert the DICOM data into any other file format like nrrd or nifti.

even in the display window, the data appears bizzare and sliced. i have attached a screenshot for reference.

Inline image

i have also tried mri convert, but the error displayed in mriconvert is that
"the data doesnt contain b-0 image" but i have checked the b-0 image option in my scanner.
can anyone plz guide me where i m doing wrong?

i have also uploaded the data on dropbox if anyone would like to check out the dicom files. here is the link:

 
 
image
 
 
 
 
 
Preview by Yahoo
 



thnx for help.

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Re: dti data dicom to nrrd/nii conversion

adeelamalik
In reply to this post by adeelamalik
Thnx for looking into matter Isaiah.

I have repetedly tried dcm2ini. It also gives me the error that "data does not contain b-0 image"
Any suggestion for a noob like me ?

Can u or anyone else plz check whether the data aquisition is correct or not ?

Thnx again.

Sent from my iPad

On 29-Jul-2016, at 12:10 AM, Isaiah Norton <[hidden email]> wrote:

Hello,

Thanks for the example data. Unfortunately, DWIConvert does not support Toshiba data right now. I will take a look at adding in the future ([1]).

For now, I can suggest to use dcm2nii [2] which *may* convert the data: it does extract the gradients, but it also prints a number of warnings.

Best,
Isaiah


On Thu, Jul 28, 2016 at 7:00 AM, Malik Adeel <[hidden email]> wrote:
i have acquired dti data from my scanner and transferred it to my mac. now the problem is that i cant convert the DICOM data into any other file format like nrrd or nifti.

even in the display window, the data appears bizzare and sliced. i have attached a screenshot for reference.

<Master Scene View.png>

i have also tried mri convert, but the error displayed in mriconvert is that
"the data doesnt contain b-0 image" but i have checked the b-0 image option in my scanner.
can anyone plz guide me where i m doing wrong?

i have also uploaded the data on dropbox if anyone would like to check out the dicom files. here is the link:

 
 
image
 
 
 
 
 
Preview by Yahoo
 



thnx for help.

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Re: dti data dicom to nrrd/nii conversion

Kikinis, Ron,M.D.
Hi,
It's not likely to happen this way, but the optimal solution would be for Toshiba to generate correct DICOMS. 
Ron

Sent from my mobile phone. 

On Jul 28, 2016, at 3:33 PM, Adeel <[hidden email]> wrote:

Thnx for looking into matter Isaiah.

I have repetedly tried dcm2ini. It also gives me the error that "data does not contain b-0 image"
Any suggestion for a noob like me ?

Can u or anyone else plz check whether the data aquisition is correct or not ?

Thnx again.

Sent from my iPad

On 29-Jul-2016, at 12:10 AM, Isaiah Norton <[hidden email]> wrote:

Hello,

Thanks for the example data. Unfortunately, DWIConvert does not support Toshiba data right now. I will take a look at adding in the future ([1]).

For now, I can suggest to use dcm2nii [2] which *may* convert the data: it does extract the gradients, but it also prints a number of warnings.

Best,
Isaiah


On Thu, Jul 28, 2016 at 7:00 AM, Malik Adeel <[hidden email]> wrote:
i have acquired dti data from my scanner and transferred it to my mac. now the problem is that i cant convert the DICOM data into any other file format like nrrd or nifti.

even in the display window, the data appears bizzare and sliced. i have attached a screenshot for reference.

<Master Scene View.png>

i have also tried mri convert, but the error displayed in mriconvert is that
"the data doesnt contain b-0 image" but i have checked the b-0 image option in my scanner.
can anyone plz guide me where i m doing wrong?

i have also uploaded the data on dropbox if anyone would like to check out the dicom files. here is the link:

 
 
image
 
 
 
 
 
Preview by Yahoo
 



thnx for help.

_______________________________________________
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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: dti data dicom to nrrd/nii conversion

inorton
In reply to this post by adeelamalik
I have repetedly tried dcm2ini. It also gives me the error that "data does not contain b-0 image"
Any suggestion for a noob like me ?
The issue appears to be that the B0 images have only the 'DiffusionGradientOrientation' (0018,9089) tag set, whereas the gradient images have both 'DiffusionGradientOrientation' and 'DiffusionBValue' (0018,9087).

I think that dcm2nii and MRIConvert require both 'DiffusionGradientOrientation' and 'DiffusionBValue' to exist, and expect 'DiffusionBValue' ~= 0 for B0 images.

Unfortunately, I don't have any experience with Toshiba diffusion images, and the data appears to have gone through some anonymization process. So, I don't know if this is a native Toshiba output convention, or an artifact of some post-processing.

You can view these tag values yourself using dcmdump [1] or the header viewer in the Slicer DICOM browser. If you are using a command-line tool, I would also suggest to sort your DICOM images using e.g. [2] or [3]

I would suggest to first discuss with the scanning tech, MR physicist, or supervising radiologist, or Toshiba support, to find out whether this is expected.

A hacky potential work-around would be to write a script to add a DiffusionBValue=0 tag whenever it is missing, using e.g. Pydicom [4].

Best,
Isaiah





 

On Thu, Jul 28, 2016 at 3:36 PM, Kikinis, Ron,M.D. <[hidden email]> wrote:
Hi,
It's not likely to happen this way, but the optimal solution would be for Toshiba to generate correct DICOMS. 
Ron

Sent from my mobile phone. 

On Jul 28, 2016, at 3:33 PM, Adeel <[hidden email]> wrote:

Thnx for looking into matter Isaiah.

I have repetedly tried dcm2ini. It also gives me the error that "data does not contain b-0 image"
Any suggestion for a noob like me ?

Can u or anyone else plz check whether the data aquisition is correct or not ?

Thnx again.

Sent from my iPad

On 29-Jul-2016, at 12:10 AM, Isaiah Norton <[hidden email]> wrote:

Hello,

Thanks for the example data. Unfortunately, DWIConvert does not support Toshiba data right now. I will take a look at adding in the future ([1]).

For now, I can suggest to use dcm2nii [2] which *may* convert the data: it does extract the gradients, but it also prints a number of warnings.

Best,
Isaiah


On Thu, Jul 28, 2016 at 7:00 AM, Malik Adeel <[hidden email]> wrote:
i have acquired dti data from my scanner and transferred it to my mac. now the problem is that i cant convert the DICOM data into any other file format like nrrd or nifti.

even in the display window, the data appears bizzare and sliced. i have attached a screenshot for reference.

<Master Scene View.png>

i have also tried mri convert, but the error displayed in mriconvert is that
"the data doesnt contain b-0 image" but i have checked the b-0 image option in my scanner.
can anyone plz guide me where i m doing wrong?

i have also uploaded the data on dropbox if anyone would like to check out the dicom files. here is the link:

 
 
image
 
 
 
 
 
Preview by Yahoo
 



thnx for help.

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Re: dti data dicom to nrrd/nii conversion

inorton
In reply to this post by adeelamalik
the resultant was 13 acquisitions with 12 dwi acquisitions and one acquisition with value b-0 each containing 36 images. now the problem is that insted of listing and renaming the data as 13 seprate series with 36 images, the scanner renames the data as one series containing 468 images. although i have tried nanaming the series after copying to mac, but the error still persists.
following is the log that dcm2ini generates:

The reason dcm2nii doesn't recognize the B0 volumes is that those images are missing the 'DiffusionBValue' tag in the DICOM header.

As a test, I sorted the images using [https://github.com/pieper/dicomsort] and then used the following script to set DiffusionBValue=0 when it is missing:

import dicom, glob
for f in glob.glob("*.dcm"):
    r = dicom.read_file(f)
    if r.has_key( dicom.tag.Tag(0x0018,0x9089)) and not r.has_key( dicom.tag.Tag(0x0018,0x9087) ):
        r.DiffusionBValue = 0
        r.save_as(f)

After doing that, the images converted OK with dcm2nii and resulting tensors looked reasonable.

Unfortunately, this is getting far in to scanner details, and I don't think we can provide much more help on this list. You will need to find someone at your institution who can either help with the scanner or help to adapt and run such a script as the above in post-processing.

Best,
Isaiah
  

On Fri, Jul 29, 2016 at 2:33 AM, Malik Adeel <[hidden email]> wrote:
the data was acquired in 12 diffusion directions to shorten the time.
the resultant was 13 acquisitions with 12 dwi acquisitions and one acquisition with value b-0 each containing 36 images. now the problem is that insted of listing and renaming the data as 13 seprate series with 36 images, the scanner renames the data as one series containing 468 images. although i have tried nanaming the series after copying to mac, but the error still persists.
following is the log that dcm2ini generates:

 Chris Rorden's dcm2nii :: 22DEC2015 32bit BSD License Carbon
Converting /Users/apple/Desktop/12 directions
Data will be exported to /Users/apple/Desktop/12 directions
Validating 469 potential DICOM images.
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dcm Error: not a DICOM image: /Users/apple/Desktop/12 directions/.DS_Store
Found 468 DICOM images.
Converting 468/468  volumes: 13
IM-0001-0001.dcm->s5024a1000.nii
GZip...s5024a1000.nii.gz
* Warning: diffusion acquisition does not have b-0 image
*  Potential partial acquisition or improper segmentation of files
*  Possible solution: check 'Collapse folders' in Help/Preferences and select directory that contains all images in subfolders
Number of diffusion directions = 12
WARNING: Unkown manufacturer - DTI BVecs are probably incorrect.
Conversion completed in 5434 ms
------------------------------------------------------------------------------------------------------------------------------------

the scanner used is "toshiba elan 1.5 T mri".
the data was not anonymised when transferred to mac from scanner.
i have uploaded a new link containing only the dti data.

link for data:



thank you for ur help again.


On Friday, July 29, 2016 2:17 AM, Isaiah Norton <[hidden email]> wrote:


I have repetedly tried dcm2ini. It also gives me the error that "data does not contain b-0 image"
Any suggestion for a noob like me ?
The issue appears to be that the B0 images have only the 'DiffusionGradientOrientation' (0018,9089) tag set, whereas the gradient images have both 'DiffusionGradientOrientation' and 'DiffusionBValue' (0018,9087).

I think that dcm2nii and MRIConvert require both 'DiffusionGradientOrientation' and 'DiffusionBValue' to exist, and expect 'DiffusionBValue' ~= 0 for B0 images.

Unfortunately, I don't have any experience with Toshiba diffusion images, and the data appears to have gone through some anonymization process. So, I don't know if this is a native Toshiba output convention, or an artifact of some post-processing.

You can view these tag values yourself using dcmdump [1] or the header viewer in the Slicer DICOM browser. If you are using a command-line tool, I would also suggest to sort your DICOM images using e.g. [2] or [3]

I would suggest to first discuss with the scanning tech, MR physicist, or supervising radiologist, or Toshiba support, to find out whether this is expected.

A hacky potential work-around would be to write a script to add a DiffusionBValue=0 tag whenever it is missing, using e.g. Pydicom [4].

Best,
Isaiah





 

On Thu, Jul 28, 2016 at 3:36 PM, Kikinis, Ron,M.D. <[hidden email]> wrote:
Hi,
It's not likely to happen this way, but the optimal solution would be for Toshiba to generate correct DICOMS. 
Ron

Sent from my mobile phone. 

On Jul 28, 2016, at 3:33 PM, Adeel <[hidden email]> wrote:

Thnx for looking into matter Isaiah.

I have repetedly tried dcm2ini. It also gives me the error that "data does not contain b-0 image"
Any suggestion for a noob like me ?

Can u or anyone else plz check whether the data aquisition is correct or not ?

Thnx again.

Sent from my iPad

On 29-Jul-2016, at 12:10 AM, Isaiah Norton <[hidden email]> wrote:

Hello,

Thanks for the example data. Unfortunately, DWIConvert does not support Toshiba data right now. I will take a look at adding in the future ([1]).

For now, I can suggest to use dcm2nii [2] which *may* convert the data: it does extract the gradients, but it also prints a number of warnings.

Best,
Isaiah


On Thu, Jul 28, 2016 at 7:00 AM, Malik Adeel <[hidden email]> wrote:
i have acquired dti data from my scanner and transferred it to my mac. now the problem is that i cant convert the DICOM data into any other file format like nrrd or nifti.

even in the display window, the data appears bizzare and sliced. i have attached a screenshot for reference.

<Master Scene View.png>

i have also tried mri convert, but the error displayed in mriconvert is that
"the data doesnt contain b-0 image" but i have checked the b-0 image option in my scanner.
can anyone plz guide me where i m doing wrong?

i have also uploaded the data on dropbox if anyone would like to check out the dicom files. here is the link:

 
 
image
 
 
 
 
 
Preview by Yahoo
 



thnx for help.

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problem compiling Slicer within Bender on Windows with MSVC 2012 - build issue with ITKVTK glue

Audette, Michel A.

Dear Slicer users, 


I am having problems building the Bender source code on Windows with MS Visual Studio 2012 due to issues with Slicer. First, I was having NumPy problems, but that went away with an CMake instruction disabling NumPy in Slicer. At this point I'm still seeing another problem in the Slicer build portion... 


CMake Error at C:/Bender/BenderBuild/Slicer-build/ITKv4/CMake/ITKModuleAPI.cmake:50 (message):
2>      No such module: "ITKVtkGlue"

Can anyone suggest a fix? I could not find the appropriate line in the Cmake files... Thanks for your support. 


Best wishes, 


Michel Audette, Ph.D.
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.

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