Hello,
This is changed in the applywarp from FSL 4.1.5,
Many Regards
Matthew
> Dear Jesper,
>
> I am using version FSL 4.1.4 when i type in the following command "applywarp -i np20_te5 -r MNI152_T1_1mm -o te5_resamp --superlevel=1" or "applywarp -i np20_te5 -o te5_resamp --superlevel=1" i get the following error message
>
> The following COMPULSORY options have not been set:
> -w,--warp filename for warp/coefficient (volume)
>
> Part of FSL (build 414)
> applywarp (Version 1.2)
>
> or
>
> The following COMPULSORY options have not been set:
> -r,--ref filename for reference image
> -w,--warp filename for warp/coefficient (volume)
> ***************************************************
>
> Part of FSL (build 414)
> applywarp (Version 1.2)
>
>
> If you type applywarp does the -w come up as
> compulsary or optional?
>
> applywarp
>
> The following COMPULSORY options have not been set:
> -i,--in filename of input image (to be warped)
> -r,--ref filename for reference image
> -w,--warp filename for warp/coefficient (volume)
> -o,--out filename for output (warped) image
>
> Thanks
>
> venkat
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library on behalf of Jesper Andersson
> Sent: Thu 5/6/2010 6:05 PM
> To: [log in to unmask]
> Subject: Re: [FSL] FNIRT- T2 weighted images between subjects
>
> 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
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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
> its entirety, whether electronic or hard copy. Thank you.
>
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