Hi Ankita,

No one has responded to this query yet and thank you for your response.

I am selecting following files as my inputs:

Main inputs:
1. T1_SPGR and Flair image
2. Atlas to use: No lesions
3. Output images: hard segmentations+memberships
4. Output max membership classification/ Correct inhomogeneity/ Output inhomogeneity field: unchecked

Atlas file:
By default Atlas file with lesions, no lesion T1 and flair fields had pre-selected *.txt files and no lesion T1 only was empty. I kept the default *txt for Atlas file with lesions, no lesion T1 and flair and selected "/mipav/plugins/Atlas/lesionToads-atlas-2012/cruise-atlas-12obj-toads2012.txt" file for no lesion T1 only. Following are all the files
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 lesion options and Advance options tabs I have kept the defaults.

Can you please suggest if I have entered wrong inputs or if anything is missing?

Thanks,
Sneha