Error while opening Dicom files

[Lucian Mircea Sasu]

Hi all,

I am using ITK snap 4.0.1 under linux ubuntu. When I try to read 6 dicom files, I get the error:

Cannot create std::vector() larger than max_size(), as in the attached screenshot.

Under Windows, for the same input, I get:

What should I do?

Lucian

[Jilei Hao]

Hi Lucian,

Thanks for reporting the issue! Have you tried converting it to nifti or nrrd and load again? 

It would also be great if you could provide a sample image for us to troubleshoot.

Best,

Jilei

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[Lucian Mircea Sasu]

Hi Jilei,

Thanks for reply. 

1. Which approach do you suggest for conversion? Which software? 

2. I am afraid I cannot give those samples, as they include personal data (GDPR). 

As a side note, I was able to read it in Simple ITK. 

Regards,

Lucian

[Jilei Hao]

You could try using c3d: https://github.com/pyushkevich/c3d/blob/master/doc/c3d.md#-dicom-series-read-read-a-dicom-image-series

And if Simple ITK works, you can also use it to read the series and write as nifti.

Best,

Jilei

To view this discussion on the web visit https://groups.google.com/d/msgid/itksnap-users/287f423c-6194-4ae4-9be1-28a139862494n%40googlegroups.com.

[Lucian Mircea Sasu]

Hi Jilei,

The same images can be read in nifti format, after conversion. 

Thanks,

Lucian

[Lucian Mircea Sasu]

BTW, I downgraded ITK to 3.6 and it is able to load those DICOM files, for which the original post reported the error. However, the echography is very foggy, compared to their nifti equivalents. 3.8 and 4.01 crashes as in the original post. 

dicom:

nifti:

Is there a setup for dicom images? both images below come from itk snap 3.6.

Kind regards,

Lucian 

[Jilei Hao]

I still need to investigate the size error, not started yet, but it's on my list.

Could the fogginess be caused by contrast settings?

Best,

Jilei

To view this discussion on the web visit https://groups.google.com/d/msgid/itksnap-users/4664d9c8-cf9e-4f7a-abcb-416558f76b0cn%40googlegroups.com.

[Lucian Mircea Sasu]

Hi Jilei,

Contrast setting helped, thanks. 

Lucian

[Jussi Tuomi]

Hi,

I'm a Windows user and I get the same error message with ITK-SNAP 4.0.1: "Error exception occured during image IO. Exception: vector too long." Tried to open 4D ultrasound image taken with GE Vivid E95 machine. It's phantom data so here's the link to the file:

https://www.dropbox.com/s/dqqn7kp2izaqymv/00657975?dl=0

Jussi

[Lucian Mircea Sasu]

Hi Jilei,

I uploaded at https://www.dropbox.com/scl/fi/l8ajzwce1uo08m4pojsyv/TT084901.ZIP?dl=0&rlkey=gc19u2min8rsmsrmfh7v19i0a a set of dicom files which cannot be opened in itk snap 4.0.1 (windows 10 and ubuntu 22.04) but can be read in itk 3.6. 

Kind regards,

Lucian

[Jilei Hao]

Thanks so much Jussi and Lucian! I'm able to replicate the error on my end and will work on a fix. The data is extremely helpful!

Best,

Jilei

[Lucian Mircea Sasu]

Thanks for feedback. How will we find out when the fix is done?

Lucian

[Jilei Hao]

It will come in a bug fix patch or a major version release, which will be announced in the user group.

Best,

Jilei

To view this discussion on the web visit https://groups.google.com/d/msgid/itksnap-users/fd7f3bfd-54bd-4ad0-a76d-018ad6961e15n%40googlegroups.com.

[Lucian Mircea Sasu]

Hi Jilei,

I was wondering whether there is any progress/fix for the bug reported in this thread. 

Best,

Lucian 

[Jilei Hao]

Hi Lucian,

Sorry for the late reply. The fix has already been merged to rel_4.0 branch. It will be included in the upcoming 4.0.2 release, which will happen around next week or so. 

Best,

Jilei

To view this discussion on the web visit https://groups.google.com/d/msgid/itksnap-users/f307ed54-03ff-430b-9160-be322c3caa89n%40googlegroups.com.