Thanks Steve for your kind clarification, I will follow your suggestion of choosing a high quality reference image and do my registration.
Thanks a lot.
venkateswaran
________________________________
From: FSL - FMRIB's Software Library on behalf of Steve Smith
Sent: Thu 3/19/2009 7:51 AM
To: [log in to unmask]
Subject: Re: [FSL] FLIRT on images with gaps between slices
Hi - when you have slice gaps this should simply reflected in the
voxel dimension in the header, which should be the summation of the
slice size plus the gap - i.e., should be the distance from the start
of one slice to the start of the next. You should not insert gappy-
data-slices into the actual image.
A separate point is that in general you should use the higher-quality
image as the reference image, and if necessary then invert the
resulting transformation before applying that.
Cheers.
On 18 Mar 2009, at 16:15, Rajagopalan, Venkateswaran wrote:
> Dear FSL users,
>
> I want to register two images for instance my Reference image
> is :Image_1 and input image is Image_2 both acquired with same in
> plane resolution of 0.98*0.98*4mm but in the case of reference image
> i.e.Image_1 the FOV was chosen to cover only a part of head,so i
> have only few slices with slice gaps of 4mm thickness introduced in
> this acquisition, whereas Image_2 on the other hand was acquired
> contiguously without any slice gap covering the entire head. I want
> to register my Image_2 to Image_1 space, so my question is can i
> directly feed them into FLIRT and FLIRT will take care of this slice
> gap problem during registration or for instance do i need to insert
> zero padded images for the missing slices in my Image_1 and do the
> registration.
>
> Thanks in advance,
>
> Regards
> venkateswaran
>
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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Cleveland Clinic is ranked one of the top hospitals
in America by U.S. News & World Report (2008).
Visit us online at http://www.clevelandclinic.org for
a complete listing of our services, staff and
locations.
Confidentiality Note: This message is intended for use
only by the individual or entity to which it is addressed
and may contain information that is privileged,
confidential, and exempt from disclosure under applicable
law. If the reader of this message is not the intended
recipient or the employee or agent responsible for
delivering the message to the intended recipient, you are
hereby notified that any dissemination, distribution or
copying of this communication is strictly prohibited. If
you have received this communication in error, please
contact the sender immediately and destroy the material in
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