Thanks, that's clarified things.
Couple more questions:
1 - are the .img and .hdr files saved in the reg directory (e.g.,
example_func.hdr, highres.hdr, etc.) just the original input files
2 - I've noticed that for each .mat file, there is the opposite, e.g.,
there is example_func2initial_highres.mat and
initial_highres2example_func.mat. Why is this?
From: Mark Jenkinson [mailto:[log in to unmask]]
Sent: Wednesday, September 22, 2004 5:00 PM
To: [log in to unmask]
Subject: Re: [FSL] Extracting registered images from FEAT
Actually only three registrations are done - those in
steps 1, 2 and 4. Step 3 is a concatentation of 1 & 2.
And step 5 is a concatenation of 1 & 2 & 4.
So to check the registrations the essential ones are
1, 2 and 4. To generate resampled images you can use
flirt with the -applyxfm and -init flags to just
apply a previously saved matrix. In this mode flirt
does not try to find a registration solution it just
applies the saved transform.
As for convert_xfm and slicer - convert_xfm is used for
concatenting matrices (which is just matrix multiplication),
inverting matrices and converting them to medx forms.
Slicer is used to create the 2D images that are shown
in the feat report.
Hope this answers your questions.
All the best,
On 22 Sep 2004, at 00:58, Fornito, Alexander wrote:
> Just to clarify, are you saying that each of the first 4 steps are
> actually separate independent registrations (i.e., none of the steps
> depends on what happens in the preceding steps, eg., the step 3
> registration does not use any information from the step 1
> and then the final step is a registration of the task epi to the
> template using a concatenation of the transformation matrices from the
> preceding 4 registrations?
> If so, then if I wanted to check each registration step in medx (for
> which I would require the registered .img and .hdr, then I would just
> run a series of standard flirt registrations?
> Can you then explain to me what the "convert_xfm" and "slicer"
> do in the scripting?
> Sorry to be a pain, I'm just tryaing to get a handle on exactly what
> Thanks again,
> -----Original Message-----
> From: Stephen Smith [mailto:[log in to unmask]]
> Sent: Saturday, September 18, 2004 5:03 PM
> To: [log in to unmask]
> Subject: Re: [FSL] Extracting registered images from FEAT
> Hi - it's probably simpler than you're imagining - actual
> are only run for each incremental pair of images, namely your steps
> 1,2,3,4 are actual registrations, and are all displayed on the report
> page. Any other transforms (eg 5) are created by mathematical
> concatenation of matrices and don't need any further checking if 1-4
> For any given transform, if you don't have a saved image that you want
> evaluate, you can take an input image, a reference image, and apply a
> saved transform with FLIRT without re-estimating the transform, using
> -applyxfm -init <transform>
> On Fri, 17 Sep 2004, Alex Fornito wrote:
>> I'm registering me task EPI via a wholehead EPI (6 DOF), the person's
>> structural (7 DOF), and then to the template (12 DOF). The FEAT
>> gives visual overlays for 4 registrations:
>> 1- task EPI to wholehead EPI
>> 2- wholehead EPI to highres structural
>> 3- task EPI to highres structural
>> 4- highres structural to template
>> 5- task epi to template
>> I understand the rationale for registering the task epi to the
>> structural via the wholehead epi, and the then to the template via
>> highres structural, but could you please explain the steps, and what
>> happens (e.g., which transformation matrices get applied to what and
>> why?). I've had a bit of trouble working it out from the scripts in
>> the .log file.
>> Also, I've noticed FEAT spits out the .mat files, but is it possible
>> extract the registered images, so that I can overlay them (as per the
>> images above) in medx and check the registration in more detail?
>> Appreciate your help,
> Stephen M. Smith DPhil
> Associate Director, FMRIB and Analysis Research Coordinator
> Oxford University Centre for Functional MRI of the Brain
> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve