ITK SNAP lesion mask files to FSL software

[Zoe Tsagaris]

Hello-

 

We are using ITK snap for developing lesion masks at my facility. 

However, our colleagues are using FSL and are unable to open the lesion mask files we send. 

Do you have suggestions for file type or conversion strategies to assist with this?

 

Thank you!

Zoe

[Sandhitsu Das]

If you save in the nifti (.nii) format, FSL programs should be able to read it.

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[Zoe Tsagaris]

Thank you for your response.

 

Our colleagues are saying:

It seems that ITK-SNAP saves it in a format that our software programs (FSL & MRIcron) don’t recognize.  Your saved files have a fourth dimension that gets added per a query in fslinfo.  

[Sandhitsu R Das]

I have not seen what your colleagues describe. It may be helpful to see the output of fslinfo on a .nii file that you save by using Save->Save Segmentation Image.

[Philip A Cook]

For a 3D image, fslinfo will show the fourth dimension with one component.

Some programs have problems with SNAP's segmentation files because they don't support unsigned integers (NIFTI data type DT_UINT16 = 512)

Assuming your labels can be represented as signed 16-bit integers (ie, all labels are less than or equal to 32767), you can do

fslmaths snapLabels.nii.gz shortLabels.nii.gz -odt short