Dear Venkat,
> Thanks very much, this may be a stupid question, i know that in
> FLIRT i can specify my output/required volume size and resample my
> image, how to do this in applywarp for instance i used MNI152_1mm as
> reference volume but i need warpvol/coefvol for the -w field. Any
> suggestions.
you make me a little uncertain now. The latest version of applywarp
doesn't require a warp or coefvol, precisely so that it can be used
for cases like this. If you type applywarp does the -w come up as
compulsary or optional?
Jesper
>
> Thanks very much
>
> venkat
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library on behalf of Jesper Andersson
> Sent: Wed 5/5/2010 5:06 AM
> To: [log in to unmask]
> Subject: Re: [FSL] FNIRT- T2 weighted images between subjects
>
> Dear Venkat,
>
>> Thanks very much does the same confirguration file work for T2
>> weighted images too. Out T2 w images are 1*1*4. Any suggestions to
>> tweak some parameters. thanks again.
>
> it shouldn't matter if it is T1 or T2 (as long as you register like
> with like of course). What might matter a little is that your voxels
> are quite anisotropic. The configuration file I sent stops at a sub-
> sampling level of 2, i.e. had you had 1x1x1mm voxels it would have
> worked with 2x2x2mm averaged voxels at the highest level. That means
> that in your case it would use 2x2x8mm voxels at the highest level,
> and I am a little concerned that might lead to poor results in the z-
> direction.
>
> The simplest thing I would suggest would be for you to use applywarp
> to supersample your images up to 1x1x1mm resolution. As you do so make
> sure to use spline interpolation. After that you can use the
> configuration file I sent to perform the registration with fnirt,
> generating warp files. And then you apply those warp files to the
> original (non-supersampled) images.
>
> I hope that was clear.
>
> Jesper
>
>
>>
>> venkat
>>
>> ________________________________
>>
>> From: FSL - FMRIB's Software Library on behalf of Jesper Andersson
>> Sent: Tue 5/4/2010 12:40 PM
>> To: [log in to unmask]
>> Subject: Re: [FSL] FNIRT- T2 weighted images between subjects
>>
>>
>> Dear Venkat,
>>
>> the following configuration file works well for registering high-
>> resolution T1 weighted images to one another. If you have a
>> reasonable high resolution (~1mm) and reasonably isotropic voxels I
>> think it should work well for you. Please let me know how it works.
>>
>>
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>
>
>
> ===================================
>
> P Please consider the environment before printing this e-mail
>
> Cleveland Clinic is ranked one of the top hospitals
> in America by U.S.News & World Report (2009).
> 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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