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
>
>
>
>
>
>
>
>
>
>
