ITK-SNAP segmentation fault for certain Siemens MRI data

[Donnie Cameron]

Hi all,

I was hoping you might be able to help with an image i/o problem I've come across in the last few weeks... I've been acquiring 4D MRI data using a Siemens scanner (software VE11C) and exporting them in DICOM format. So far so good. But when I try to open them in ITK-SNAP, some of the data (which all have the same dimensions, acquisition, etc.) cause the application to bomb out without any error message. 

I've tried loading the data using the 'Open image' button in the GUI, dragging and dropping the folder into the GUI, and using the command line tool. ITK-SNAP does seem to recognise the images as a 'DICOM image series' in the 'Open image' dialog, and shows the correct image dimensions in the 'Select DICOM series to open' window, but crashes before the images are loaded and the 'Image summary' is shown. The command line approach gives some sort of error message at least - a single-line 'Segmentation fault'.

Changing the extension of the DICOM files does not help (they have no extension on export, but this is not a problem for most of my datasets). Other than that, I'm running out of ideas!

Any suggestions for how I can get to the bottom of this issue?

Many thanks,
Donnie

[mohammad ghorbani]

Hi Donnie,

Have you considered converting the DICOM images to NIFTI format before loading them into ITK-SNAP? This might help resolve the issue you’re encountering. Try using MRIcro software to convert your DICOM images to NIfTI.

Regards,
Mohammad