if you can skull strip them you should be able to run the stream afterwards. I've never seen an image with the background so high though - it's something you should try to fix on the acquisition end. On Wed, 28 Feb 2007, Anil Roy wrote:

Yes, if I just run the raw files, then the brain crashes so I don't get any output. But the background values are high in the orig.mgz file also and the xfm is not accurate.

afni however is able to process all these raw files without a problem including the talairach and skull strip.

Is there some flag or something that I have to use or is there no way to fix this.

Thanks,

Anil.

On 2/28/07, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

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hmmm, the high background is there in the 001.mgz also, so it's not an afni thing. Do you see this in all your images?

On Tue, 20 Feb 2007 aroy85@gmail.com wrote:

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The following files have been uploaded to the Martinos Center FileDrop

site

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by Anil Roy for you to download:

(1) 001.mgz

These files will expire in 30 days.

To view or download these files, go in your web browser to:

https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/5075/89/4def6e08...

...

DO NOT SHARE this web address with anyone else. It is your personal

access key to the files.

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Overall Comment about files from Anil Roy:

Bruce, Here is the 001.mgz