Converting dual echo DICOM to NRRD (PD/T2)

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Converting dual echo DICOM to NRRD (PD/T2)

azaitsev
Hello:

I am looking for the replacement of FreeSurfer mri_convert utility with
Slicer modules.

The DicomToNrrdConverter works fine for single echo images

This is not a case for dual echo images (PD/T2 in our case) since there
is no analogue for FreeSurfer frame number argument (-f #).

When applying without "frame number" argument, the DicomToNrrdConverter
acknowledges that there are two volumes and the resulting volume is
about twice as big as a single echo volume.

How do I split the resulting NRRD volume on two sub-volumes?
The unu utility documentation does not provide help with extraction
sub-volume from specific frame.

Sorting original DICOM folder files by echo number is not a desirable
option.

Thank you.

Alex

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Re: Converting dual echo DICOM to NRRD (PD/T2)

pieper
Administrator
Hi Alex -

Can you post an example of the nrrd file that you get from the converter?

-Steve

On 12/03/2010 03:56 PM, Alexander Zaitsev wrote:

> Hello:
>
> I am looking for the replacement of FreeSurfer mri_convert utility with
> Slicer modules.
>
> The DicomToNrrdConverter works fine for single echo images
>
> This is not a case for dual echo images (PD/T2 in our case) since there
> is no analogue for FreeSurfer frame number argument (-f #).
>
> When applying without "frame number" argument, the DicomToNrrdConverter
> acknowledges that there are two volumes and the resulting volume is
> about twice as big as a single echo volume.
>
> How do I split the resulting NRRD volume on two sub-volumes?
> The unu utility documentation does not provide help with extraction
> sub-volume from specific frame.
>
> Sorting original DICOM folder files by echo number is not a desirable
> option.
>
> Thank you.
>
> Alex
>
> _______________________________________________
> 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: Converting dual echo DICOM to NRRD (PD/T2)

Isaiah Norton-3
In reply to this post by azaitsev
Hi Alex,
The simplest way may be to use "unu dice" command. Unu is available in Slicer as part of the teem library (though if you are using ubuntu it might be faster to just apt-get install teem-apps instead of fussing with paths.

There are some usage examples here:
http://www.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:TeemExamples

-Isaiah

On Fri, Dec 3, 2010 at 3:56 PM, Alexander Zaitsev <[hidden email]> wrote:
Hello:

I am looking for the replacement of FreeSurfer mri_convert utility with
Slicer modules.

The DicomToNrrdConverter works fine for single echo images

This is not a case for dual echo images (PD/T2 in our case) since there
is no analogue for FreeSurfer frame number argument (-f #).

When applying without "frame number" argument, the DicomToNrrdConverter
acknowledges that there are two volumes and the resulting volume is
about twice as big as a single echo volume.

How do I split the resulting NRRD volume on two sub-volumes?
The unu utility documentation does not provide help with extraction
sub-volume from specific frame.

Sorting original DICOM folder files by echo number is not a desirable
option.

Thank you.

Alex

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Re: Converting dual echo DICOM to NRRD (PD/T2)

azaitsev
In reply to this post by pieper
Hi Steve:

Here is the link:
http://www.na-mic.org/Wiki/index.php/File:PDT2_slicer.nrrd.gz

Thank you,
Alex

On Fri, 03 Dec 2010 16:38:20 -0500, Steve Pieper <[hidden email]>
wrote:

> Hi Alex -
>
> Can you post an example of the nrrd file that you get from the converter?
>
> -Steve
>
> On 12/03/2010 03:56 PM, Alexander Zaitsev wrote:
>> Hello:
>>
>> I am looking for the replacement of FreeSurfer mri_convert utility with
>> Slicer modules.
>>
>> The DicomToNrrdConverter works fine for single echo images
>>
>> This is not a case for dual echo images (PD/T2 in our case) since there
>> is no analogue for FreeSurfer frame number argument (-f #).
>>
>> When applying without "frame number" argument, the DicomToNrrdConverter
>> acknowledges that there are two volumes and the resulting volume is
>> about twice as big as a single echo volume.
>>
>> How do I split the resulting NRRD volume on two sub-volumes?
>> The unu utility documentation does not provide help with extraction
>> sub-volume from specific frame.
>>
>> Sorting original DICOM folder files by echo number is not a desirable
>> option.
>>
>> Thank you.
>>
>> Alex
>>
>> _______________________________________________
>> 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: Converting dual echo DICOM to NRRD (PD/T2)

pieper
Administrator
Hi Alex -

The following seems to work for me:

> unu dice -a 3 -i PDT2_slicer.nrrd -ff %d.nrrd -o ./
> unu dice: ./0.nrrd ...
> unu dice: ./1.nrrd ...

The unu executable is in the bin directory of the slicer3 distribution.

-Steve

On 12/06/2010 04:57 PM, azaitsev wrote:

> Hi Steve:
>
> Here is the link:
> http://www.na-mic.org/Wiki/index.php/File:PDT2_slicer.nrrd.gz
>
> Thank you,
> Alex
>
> On Fri, 03 Dec 2010 16:38:20 -0500, Steve Pieper<[hidden email]>
> wrote:
>> Hi Alex -
>>
>> Can you post an example of the nrrd file that you get from the converter?
>>
>> -Steve
>>
>> On 12/03/2010 03:56 PM, Alexander Zaitsev wrote:
>>> Hello:
>>>
>>> I am looking for the replacement of FreeSurfer mri_convert utility with
>>> Slicer modules.
>>>
>>> The DicomToNrrdConverter works fine for single echo images
>>>
>>> This is not a case for dual echo images (PD/T2 in our case) since there
>>> is no analogue for FreeSurfer frame number argument (-f #).
>>>
>>> When applying without "frame number" argument, the DicomToNrrdConverter
>>> acknowledges that there are two volumes and the resulting volume is
>>> about twice as big as a single echo volume.
>>>
>>> How do I split the resulting NRRD volume on two sub-volumes?
>>> The unu utility documentation does not provide help with extraction
>>> sub-volume from specific frame.
>>>
>>> Sorting original DICOM folder files by echo number is not a desirable
>>> option.
>>>
>>> Thank you.
>>>
>>> Alex
>>>
>>> _______________________________________________
>>> 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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