Hello everyone,

I'm trying to find a tissue segmentation map for the 4mm 'nihpd_asym' template. The preproc.sh register functional MRI images to the 'hihpd_asym_4mm' template, and I need a single gray matter mask file in this template space for all subjects. This can be a probability map with intenxity value in (0,1).

There are subject specific tissue segmentation file generated by the script, but I need a single mask for all subjects, since all subjects are already registered to the template space.

And I'm not clear where the template file is from. There is a nihpd website at UCSD, though I have no idea if that is the souce of the template file.

I appreciate any help on this issue.

Wei Liu
University of Utah

Hello Wei,

The templates used for the normalization are from here http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1. I had to do some manipulations to the files to get them into the right orientation, etc.. for the preprocessing scripts. You can download the templates that I used for the preprcessing from: http://www.nitrc.org/frs/downloadlink.php/3974.

Why don't you just average the subject specific tissue segmentations to generate your GM mask file? Files named using the format swssd{subject#}_session_{session#}_anat_gm.nii.gz are GM files in template space.

For more information on the Athena pipline, please refer to: http://www.nitrc.org/plugins/mwiki/index.php/neurobureau:AthenaPipeline

Cheers,
Cameron

Cameron,

Thanks for the information. That is really helpful. Yes, on a second thought after your reply, averaging all subjects tissure segmentation map is a good idea. I'll give it a try.

Cheers,
Wei