Dear Ankita,

Thank you for your response. I am not able to succeed until I choose *.txt file as it gives me an error that no atlas has been chosen. If I select with lesions option can you please suggect which *txt files in Atlas to use for Atlas file with lesions, no lesion T1 and flair and no lesion T1 only?

I selected following .txt files and I do not get any output.
1. Atlas file - With lesions: /mipav/plugins/Atlas/lesionToads-atlas-2012/cruise-atlas-12obj-lesiontoads2012.tx
2. Atlas file - No lesions - T1 and Flair: /mipav/plugins/Atlas/lesionToads-atlas-2012/cruise-atlas-12obj-toads2012.txt
3. Atlas File- no lesion - T1 only: /mipav/plugins/Atlas/lesionToads-atlas-2012/cruise-atlas-12obj-toads2012.txt

For main inputs I have selected:
1. Output images: hard segmentations+memberships
2. Output max membership classification/ Correct inhomogeneity/ Output inhomogeneity field: unchecked

All I get is lesion+toads.input output.

Thanks,
Sneha