From grayson at ohsu.edu  Fri Jul 29 20:50:19 2011
From: grayson at ohsu.edu (David Grayson)
Date: Fri Jul 29 20:50:26 2011
Subject: [Jip-commits] question about image alignment and registration
Message-ID: <0A6ED1643D4A794EA78829FBA1C343FD01408212DD@EX-MB01.ohsu.edu>

Hi there,

I am very excited to start using these jip tools, as we have lots of rhesus monkey functional data that we would like to put through these processing steps. I have successfully installed the tools and gone through a bunch of the documentation, but I am still a bit confused about certain things.

First off, is it possible to process raw DICOMS using these tools? I noticed in the documentation that it listed nii files under ?Image data formats? but not DICOMS. Does JIP assume a certain level of preprocessing has already taken place before you begin using its tools?

Also, is there listed anywhere an example processing stream? I?m not quite sure which commands to begin with. My intuition tells me to use the align command to align the T1 file onto a template file, and then align the epi (BOLD) scan onto the T1. I am a newcomer when it comes to building processing streams from scratch, so I?m really not sure.

Any help or advice would be tremendously appreciated.

Thank you,

David
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