Problems with data manifest file during atlas building

[Helena Gellersen]

Dear all,

I am trying to build my own atlas based on a sample of manually segmented images. I have specified the data manifest file according to the example shown on the website (https://sites.google.com/site/hipposubfields/building-an-atlas#TOC-Data-Manifest-File)  but I get the error Bad specification for atlas "CBU161126". Here is an example of the first line of the data manifest text file where <home_path> is stands for the path where I keep the data manifest file and other files needed for ashs_train.sh to work:

CBU161126 <home_path>/data/sub-CBU161126-T1.nii <home_path>/data/sub-CBU161126-highres-T2.nii <home_path>/seg/CBU161126_L.nii <home_path>/seg/CBU161126_R.nii

If anyone has an idea for why this fails, I would be very grateful!

[Paul Yushkevich]

Hi Helena,

Does your home path contain any spaces or unusual characters? If not, could you try running with the -d flag and sending me the output?

Thanks!
Paul

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Paul A. Yushkevich, Ph.D.
Associate Professor
Penn Image Computing and Science Laboratory
Department of Radiology
University of Pennsylvania

[lok.ki...@gmail.com]

I was wondering what the solution here was. I'm running into exactly the same error, and I can't figure out what's wrong with my data manifest file either.