Hi, 

I have a project were I have elderly stroke patients. I have segmented the lesion in ITK snap and saved the segmentation as a Nifti file. 
I want to use the clinical toolbox to account for the anatomy of an elderly brain and mask out the lesion. 

I´m adding the T1 image to "anatomicals" and the segmentation to "lesion maps". 

After this, I receive the following message;
The following modules did not run:
Failed: MR segment-normalize

I don´t know what I have done wrong. To the best of my understanding, I have followed the manual for the clinical toolbox. 

Just to clarify, The segmentation nifit file is only the lesion, it´s not saved upon a T1 image. And, in the same batch, I´m also running realign & unwarp as well as Coregistration. (The realign & unwarp and coregistration seemed to work out ok with no error message).

Any help would be very much appreciated!

Thank you in advance, 
Hanna

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Did you download the version from Github? Were you successfully able to run the tutorial? 

The toolbox works by aligning features of the brain (seen on a T1, FLAIR, T2 or CT scan) to a template and applying that alignment to your lesion map. The algorithm can not work with only a lesion file, as the binary lesion map has no anatomical features that correspond with the template image. I would suggest reading the manual.doc that comes with the software.