Slicer and multi-part DICOM scans

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Slicer and multi-part DICOM scans

Murat Maga

Hi all,

 

I received a dataset in which a scan has been split into three sections. I managed to use the DICOM browser to get all three datasets into slicer. However, is there a way to stitch them together into a single volume? I thought that would happen during the import.

 

Is there an easy way of doing this? More importantly can this be scripted (beginning from the DICOM import) since I have couple of hundreds of specimens scanned like this?

Thanks,

 

Murat

 


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Re: Slicer and multi-part DICOM scans

Andrey Fedorov-2
Murat, can you share a sample dataset? It is not quite clear what is going on.

On Fri, Aug 7, 2015 at 2:54 PM, Murat Maga <[hidden email]> wrote:

> Hi all,
>
>
>
> I received a dataset in which a scan has been split into three sections. I
> managed to use the DICOM browser to get all three datasets into slicer.
> However, is there a way to stitch them together into a single volume? I
> thought that would happen during the import.
>
>
>
> Is there an easy way of doing this? More importantly can this be scripted
> (beginning from the DICOM import) since I have couple of hundreds of
> specimens scanned like this?
>
> Thanks,
>
>
>
> Murat
>
>
>
>
> _______________________________________________
> 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: Slicer and multi-part DICOM scans

Murat Maga
In reply to this post by Murat Maga
Hi Andrey,
Sure. This is what I was trying with. It is about 200MB
https://www.dropbox.com/s/86es1ob3ue14vbr/USNM239883-Cranium.zip?dl=0

-----Original Message-----
From: Andrey Fedorov [mailto:[hidden email]]
Sent: Friday, August 07, 2015 8:04 PM
To: Murat Maga
Cc: SPL Slicer Users
Subject: Re: [slicer-users] Slicer and multi-part DICOM scans

Murat, can you share a sample dataset? It is not quite clear what is going on.

On Fri, Aug 7, 2015 at 2:54 PM, Murat Maga <[hidden email]> wrote:

> Hi all,
>
>
>
> I received a dataset in which a scan has been split into three
> sections. I managed to use the DICOM browser to get all three datasets into slicer.
> However, is there a way to stitch them together into a single volume?
> I thought that would happen during the import.
>
>
>
> Is there an easy way of doing this? More importantly can this be
> scripted (beginning from the DICOM import) since I have couple of
> hundreds of specimens scanned like this?
>
> Thanks,
>
>
>
> Murat
>
>
>
>
> _______________________________________________
> 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: Slicer and multi-part DICOM scans

Andrey Fedorov-2
In reply to this post by Murat Maga
Murat,

I took a look. I think the behavior of Slicer is correct, since these
are 3 different series. I don't know of an easy ready to use way to
stitch them in Slicer. If you can do a little coding, you can
calculate the bounding box of the 3 volumes and resample into one
volume. You can script loading of the DICOM series similar to how it
is done here: https://github.com/fedorov/PCampReview/blob/master/PCampReviewPreprocessor.py#L116-L151

hope this helps

AF

On Sat, Aug 8, 2015 at 1:30 AM, Murat Maga <[hidden email]> wrote:

> Hi Andrey,
> Sure. This is what I was trying with. It is about 200MB
> https://www.dropbox.com/s/86es1ob3ue14vbr/USNM239883-Cranium.zip?dl=0
>
> -----Original Message-----
> From: Andrey Fedorov [mailto:[hidden email]]
> Sent: Friday, August 07, 2015 8:04 PM
> To: Murat Maga
> Cc: SPL Slicer Users
> Subject: Re: [slicer-users] Slicer and multi-part DICOM scans
>
> Murat, can you share a sample dataset? It is not quite clear what is going on.
>
> On Fri, Aug 7, 2015 at 2:54 PM, Murat Maga <[hidden email]> wrote:
>> Hi all,
>>
>>
>>
>> I received a dataset in which a scan has been split into three
>> sections. I managed to use the DICOM browser to get all three datasets into slicer.
>> However, is there a way to stitch them together into a single volume?
>> I thought that would happen during the import.
>>
>>
>>
>> Is there an easy way of doing this? More importantly can this be
>> scripted (beginning from the DICOM import) since I have couple of
>> hundreds of specimens scanned like this?
>>
>> Thanks,
>>
>>
>>
>> Murat
>>
>>
>>
>>
>> _______________________________________________
>> 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: Slicer and multi-part DICOM scans

Steve Pieper-2
Hi Murat - 

On pretty simple thing to do is to use the CropVolume module.  I loaded all three sections and made a slice visible for all three and then dragged out the ROI to cover the extent.  Then I used AddScalarVolume to put the two extra series into the new volume.  There's a little bit of a seam as you can see in the yellow and green viewers in the second image.  But this is probably just a visual issue and probably won't impact measurements.

As Andrey points out it would be pretty straightforward to script this and also to use a direct pixel copy instead of the resampling to avoid the artefact.

HTH,
-Steve

p.s. cool gorilla skull!  is that freely shareable and can we add it to the data store?


Inline image 1
Inline image 1

On Sun, Aug 9, 2015 at 9:46 PM, Andrey Fedorov <[hidden email]> wrote:
Murat,

I took a look. I think the behavior of Slicer is correct, since these
are 3 different series. I don't know of an easy ready to use way to
stitch them in Slicer. If you can do a little coding, you can
calculate the bounding box of the 3 volumes and resample into one
volume. You can script loading of the DICOM series similar to how it
is done here: https://github.com/fedorov/PCampReview/blob/master/PCampReviewPreprocessor.py#L116-L151

hope this helps

AF

On Sat, Aug 8, 2015 at 1:30 AM, Murat Maga <[hidden email]> wrote:
> Hi Andrey,
> Sure. This is what I was trying with. It is about 200MB
> https://www.dropbox.com/s/86es1ob3ue14vbr/USNM239883-Cranium.zip?dl=0
>
> -----Original Message-----
> From: Andrey Fedorov [mailto:[hidden email]]
> Sent: Friday, August 07, 2015 8:04 PM
> To: Murat Maga
> Cc: SPL Slicer Users
> Subject: Re: [slicer-users] Slicer and multi-part DICOM scans
>
> Murat, can you share a sample dataset? It is not quite clear what is going on.
>
> On Fri, Aug 7, 2015 at 2:54 PM, Murat Maga <[hidden email]> wrote:
>> Hi all,
>>
>>
>>
>> I received a dataset in which a scan has been split into three
>> sections. I managed to use the DICOM browser to get all three datasets into slicer.
>> However, is there a way to stitch them together into a single volume?
>> I thought that would happen during the import.
>>
>>
>>
>> Is there an easy way of doing this? More importantly can this be
>> scripted (beginning from the DICOM import) since I have couple of
>> hundreds of specimens scanned like this?
>>
>> Thanks,
>>
>>
>>
>> Murat
>>
>>
>>
>>
>> _______________________________________________
>> 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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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.