Thanks Matthew i will upgrade.
venkat
________________________________
From: FSL - FMRIB's Software Library on behalf of Matthew Webster
Sent: Fri 5/7/2010 11:19 AM
To: [log in to unmask]
Subject: Re: [FSL] FNIRT- T2 weighted images between subjects
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 <http://www.clevelandclinic.org/> for
>> a complete listing of our services, staff and
>> locations.
>>
>>
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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 <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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> and may contain information that is privileged,
> confidential, and exempt from disclosure under applicable
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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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