On Mon, Jan 5, 2009 at 3:35 PM, Matt Glasser <[log in to unmask]> wrote:

Because you are wanting to resample V1, a vector image, you should use
vecreg so you don't get artifacts. I don't know if by default it does an
identity transform like FLIRT or not, but if so you can use it in the same
way as Mark suggests you use FLIRT.

Peace,

Matt.

-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf

Of Mark Jenkinson
Sent: Monday, January 05, 2009 5:06 PM
To: [log in to unmask]
Subject: Re: [FSL] dtifit V{1,2,3} data format

Hi,

That's right - although you can leave out the -init and identity
matrix as this is the default.

All the best,
Mark

On 5 Jan 2009, at 22:52, Siddharth Srivastava wrote:

> Hi Matt,
> Thanks for the response. Just to confirm, for a
> resampling of V1 (say) to structural, with no registration:
> flirt -in <the V1 image set> -out <resamples V1 image set> -ref
> <structural> -applyxfm -init <identity matrix.mat> ?
> thanks,
> sid.
>
>
> On Wed, Dec 31, 2008 at 1:08 PM, Matt Glasser <[log in to unmask]> wrote:
> Your input image will be resampled to the same dimensions as the
> reference image. If you do not want any spatial transformation of
> the image, you can use an identity matrix as the <mytransform> in
> the below example.
>
>
> Peace,
>
>
> Matt.
>
>
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf Of Siddharth Srivastava
> Sent: Wednesday, December 31, 2008 2:55 PM
> To: [log in to unmask]
> Subject: Re: [FSL] dtifit V{1,2,3} data format
>
>
> Hi saad,
> Thanks again. I am aware of the issue while transforming
> vector images. However, for my specific problem,
> my DTI data and metrics are already in register with the
> structurals, it is just that they are of different dimensions
> and voxel size. I needed to equalize for these two parameters only,
> and hence i wanted to reslice them to the
> structurals. Can i do it in fsl, for the 4D data as input, and 3D
> data (T1) as target?
> regards,
> sid.
>
> On Wed, Dec 31, 2008 at 10:28 AM, Saad Jbabdi <[log in to unmask]>
> wrote:
>
> Hi Sid
>
>
> If you want to transform vector images (such as V1,2,3) onto
> structural space, you can use the FSL command-line tool called
> "vecreg".
>
>
> You need to be careful when transforming vector images, as any
> rotation to the image must be applied to the vectors as well (See
> the FDT documentation).
>
> Note that vecreg doesn't calculate a transform for you, but uses a
> transform given as an output of FLIRT or FNIRT.
>
>
> For example, you may do the following:
>
> > flirt -in <b0image> -ref <structural> -omat <mytransform>
>
> > vecreg -i <V1> -o <V1_to_struct> -r <structural> -t <mytransform>
>
>
> Cheers,
>
> Saad.
>
>
> On 31 Dec 2008, at 18:06, Siddharth Srivastava wrote:
>
>
>
> Hi saad,
> Thanks for the reply. since this mail was sent, i have
> learnt about
> fslsplit and merge. I wanted to reslice/resample the metrics (V1 et
> al.) to my
> structurals, which i do in spm. Hence i needed to exctract each
> component,
> change them to .img, reslice, and finally merge them into the nii.gz
> format
> (to be used by ITK SNAP). I am sure there is an easier way in FSL to
> do the
> same thing without going through the conversion. Is there? an
> equivalent of
> reslice/resample command in FSL?
> best regards, and a happy new year!
> sid.
>
> On Wed, Dec 31, 2008 at 8:08 AM, Saad Jbabdi <[log in to unmask]>
> wrote:
>
> Hi Sid,
> Sorry for such a late reply!
> Yes the V<i> files are in 4D format.
> In order to extract the x,y,z components, you can use fslsplit.
> For example:
>
> > fslsplit outputs_V1 components
>
> In which case the x,y,z components of V1 will be respectively:
> components0000.nii.gz
> components0001.nii.gz
> components0002.nii.gz
>
> Cheers,
> Saad.
>
>
>
> On 19 Dec 2008, at 00:25, Siddharth Srivastava wrote:
>
> Hi list,
> I am sure this has been discussed before, as it is a very
> basic newbie question. I am trying to find out where the 3
> components of the principal directions are stored? The dtifit
> command outputs _V{1,2,3}.nii.gz . is each nii.gz file in a 4d
> format, having V1x, V1y and V1z components? How do i go about
> extracting these components into seperate img files?
> Thanks,
> sid.
>
>
> Saad Jbabdi
> Oxford University FMRIB Centre
>
> JR Hospital, Headington, OX3 9DU, UK
> +44 (0) 1865 222545 (fax 717)
> www.fmrib.ox.ac.uk/~saad
>
>
>
> Saad Jbabdi
>
> Oxford University FMRIB Centre
>
>
> JR Hospital, Headington, OX3 9DU, UK
>
> +44 (0) 1865 222545 (fax 717)
>
> www.fmrib.ox.ac.uk/~saad
>
>
>
>
>
>
>
>
>
>