Krish,
gotcha, thanks for clarifying.
Jason
________________________________
From: FSL - FMRIB's Software Library on behalf of Dr Krish Singh
Sent: Thu 7/22/2004 10:40 AM
To: [log in to unmask]
Subject: Re: [FSL] Negative voxel dimensions and Flirt/Fast
Hi jason,
Sorry my post below was a tad confusing (mixing up Flirt and Fast!).
I did start with a positive voxel size. It became negative when I ran the
data through Flirt (this is absolutely expected). Then it became positive
again when I ran the output of Flirt through Fast (not expected).
Krish
On 22/7/04 3:26 pm, "Jason Craggs" <[log in to unmask]> wrote:
> Krish,
>
> perhaps I am missing something.
> How is it that you started with a negative voxel size?
> By definition does it not have to be positive?
>
> Jason
>
> ________________________________
>
> From: FSL - FMRIB's Software Library on behalf of Dr Krish Singh
> Sent: Thu 7/22/2004 10:23 AM
> To: [log in to unmask]
> Subject: Re: [FSL] Negative voxel dimensions and Flirt/Fast
>
>
>
> Hi Jason,
>
> Thanks for your reply.
>
> My point was that I had a registered image with -2,2,2, which I am happy
> with. Its just that when this image was run through Flirt the resulting
> images had voxel dimensions of +2,2,2, which seems inconsistent.
>
> All the best,
>
> Krish
>
>
>
>
>
> On 22/7/04 3:20 pm, "Jason Craggs" <[log in to unmask]> wrote:
>
>> Kirsh,
>>
>> It is my understanding that, regardless of the input image, FSL will convert
>> it to match the registered/target image.
>> So, if your raw image was 1*1*1 and the template image is 2*2*2, your final
>> image will indeed be 2*2*2.
>> If I am wrong someone please correct me. It is for this reason that we have
>> developed our own template isovoxeled image.
>>
>> Jason
>>
>>
>>
>> ________________________________
>>
>> From: FSL - FMRIB's Software Library on behalf of Dr Krish Singh
>> Sent: Thu 7/22/2004 10:13 AM
>> To: [log in to unmask]
>> Subject: [FSL] Negative voxel dimensions and Flirt/Fast
>>
>>
>>
>> Hi there,
>>
>> I've got myself into some laterality difficulties with negative voxel
>> dimensions. Let me explain what I did:
>>
>> 1) Using flirt I registered a radiological axial volume to the FSL T1
>> template. avwhd now reports that this has voxel dimensions of -2,2,2 mm
>> which is correct I think.
>>
>> 2) I took the registered volume generated in the above step and passed it
>> through Flirt to generate segmentation maps. avwhd now reports that the
>> voxel dimensions for the segmented images are 2,2,2 which I don't think is
>> correct as they should be the same as the input image.
>>
>> Is the above behaviour expected? It causes me some problems because my
>> software, mri3dX, assumes that if you overlay one volume on another and
>> their horizontal voxel dimensions have different signs, then it needs to
>> flip the laterality of the overlay. In the case of the above, this is
>> clearly not the case.
>>
>> All the best,
>>
>> Krish
>>
>> --
>> Dr K.D. Singh
>> Senior Lecturer and Convenor of the Neuroimaging Research Group,
>> Director, MRI Research Centre,
>> Neurosciences Research Institute
>> Aston University, Birmingham B4 7ET, U.K.
>> Tel/Fax: +44 (0)121 [204 3865/3864]/[333 4220]
>> [log in to unmask], http://www.aston.ac.uk/lhs/staff/singhkd/
>>
>
> --
> Dr K.D. Singh
> Senior Lecturer and Convenor of the Neuroimaging Research Group,
> Director, MRI Research Centre,
> Neurosciences Research Institute
> Aston University, Birmingham B4 7ET, U.K.
> Tel/Fax: +44 (0)121 [204 3865/3864]/[333 4220]
> [log in to unmask], http://www.aston.ac.uk/lhs/staff/singhkd/
>
--
Dr K.D. Singh
Senior Lecturer and Convenor of the Neuroimaging Research Group,
Director, MRI Research Centre,
Neurosciences Research Institute
Aston University, Birmingham B4 7ET, U.K.
Tel/Fax: +44 (0)121 [204 3865/3864]/[333 4220]
[log in to unmask], http://www.aston.ac.uk/lhs/staff/singhkd/
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