On Wednesday 01 April 2009 21:13, MCLAREN, Donald wrote:
> While it was originally written written to import c1, c2, and c3 files;
> there is no requirement that the images be segments.
>
> We've used the function for DTI data as well.
>
> It should be noted that DARTEL can't use fMRI data to create the
> deformation field, but that by importing another modality into DARTEL the
> same way as segments, then the deformations can be applied.
>
> This is true, at least, for DTI data
>
> On Wed, Apr 1, 2009 at 3:04 PM, John Ashburner
<
[log in to unmask]>wrote:
> > If you have the imported GM and WM (rc1 and rc2) files, then you would
> > run DARTEL using these. If I remember correctly the "import_for_dartel.m
> > function was to take c1 and c2 images, and do the necessary tweaks to
> > obtain
> > the rc1 and rc2 images that DARTEL can work with. You would not apply it
> > to
> > the fMRI data.
> >
> > Best regards,
> > -John
> >
> > On Wednesday 01 April 2009 19:19, Amir Tahmasebi wrote:
> > > Hi John,
> > >
> > > I used the "import_for_dartel.m" file from another posting dated on
> > > Wed. 6 Feb. 2008.
> > >
> > > Regards,
> > > Amir
> > >
> > > John Ashburner wrote:
> > > > I'm not quite sure what you mean by " use the code provided by John
> > > > to transfer both fMRI and structural data to DARTEL space". If this
> > > > means using the create DARTEL warped images, then then doing this
> > > > again to
> >
> > the
> >
> > > > contrast images (step 4) is going to move the data out of alignment.
> > > >
> > > > If you have SPM8b (soon to be SPM8), then maybe try skipping the "use
> >
> > the
> >
> > > > code provided by John" step. Generate the contrast images in native
> > > > space (without smoothing), and simply warp them using the new
> >
> > "Normalise
> >
> > > > to MNI space" option of DARTEL.
> > > >
> > > > Best regards,
> > > > -John
> > > >
> > > > On Wednesday 01 April 2009 18:24, you wrote:
> > > >> Dear John and SPMers,
> > > >>
> > > >> I am facing a problem while performing DARTEL-based normalization of
> >
> > my
> >
> > > >> fMRI data followed by group analysis.
> > > >>
> > > >> I followed the below routine to conduct first level and second level
> > > >> analysis on my fMRI data:
> > > >>
> > > >> (1) coregister fMRI and structural for each subject
> > > >> (2) perform DARTEL among segmented structural data
> > > >> (2) use the code provided by John to transfer both fMRI and
> > > >> structural data to DARTEL space
> > > >> (3) perform first-level analysis of the fMRI data --> output: con
> >
> > files
> >
> > > >> (4) in order to perform second level analysis, I apply DARTEL
> >
> > parameters
> >
> > > >> to warp my con files (using "create warp").
> > > >>
> > > >> The problem is at step 4: the warped con images seems not to have
> > > >> correct orientation. However, if I apply the same parameters to the
> >
> > fMRI
> >
> > > >> data that are transformed to DARTEL space (from step 2), the data
> > > >> look OK.
> > > >>
> > > >> Is there anything that I am missing?
> > > >>
> > > >> Thank you,
> > > >>
> > > >> Regards,
> > > >> Amir
> > > >>
> > > >> John Ashburner wrote:
> > > >>> This will be straightforward in SPM8 - and it will combine the
> > > >>> transforms with an affine transform so that the spatially
> > > >>> normalised images are in MNI space, rather than the population
> > > >>> average. SPM8
> >
> > will
> >
> > > >>> be released very soon, but I think the necessary routines are
> > > >>> already available in the recent updates for SPM8b.
> > > >>>
> > > >>> An alternative strategy could be to spatially normalise contrast
> >
> > images
> >
> > > >>> from a first level analysis done in native space, prior to doing
> > > >>> the 2nd level analysis. This could be done one scan per subject.
> > > >>>
> > > >>> Best regards,
> > > >>> -John
> > > >>>
> > > >>> On Monday 30 March 2009 17:24, Amir Tahmasebi wrote:
> > > >>>> Dear John,
> > > >>>>
> > > >>>> I am using DARTEL to warp fMRI data. Using DARTEL's "create
> > > >>>> warped" tool, for every image you have to provide one flow field.
> > > >>>> Is there
> >
> > any
> >
> > > >>>> way that I can apply one flow field to a bunch of images at once?
> > > >>>>
> > > >>>> Thank you,
> > > >>>>
> > > >>>> Regards,
> > > >>>> Amir
> > > >>>>
> > > >>>> John Ashburner wrote:
> > > >>>>> DARTEL is run as described in the user guide, but there is an
> > > >>>>> extra option that allows the resulting deformations to be
> > > >>>>> automatically combined with an additional affine transform. The
> > > >>>>> DARTEL warps encode the inter-subject variability, and the affine
> > > >>>>> transform
> >
> > warps
> >
> > > >>>>> the average of the population to MNI space.
> > > >>>>>
> > > >>>>> Best regards,
> > > >>>>> -John
> > > >>>>>
> > > >>>>> On Tuesday 24 March 2009 17:49, Amir Tahmasebi wrote:
> > > >>>>>> Hi John,
> > > >>>>>>
> > > >>>>>> Thanks for your reply.
> > > >>>>>>
> > > >>>>>> Does this mean that the fMRI data are only affinely registered
> > > >>>>>> between subjects?
> > > >>>>>>
> > > >>>>>> Regards,
> > > >>>>>> Amir
> > > >>>>>>
> > > >>>>>> John Ashburner wrote:
> > > >>>>>>> If you have SPM8b (latest updates), then you should find this
> >
> > much
> >
> > > >>>>>>> easier, as there is now an option to spatially normalise (and
> > > >>>>>>> spatially blur) fMRI to MNI space (as it incorporates an
> >
> > additional
> >
> > > >>>>>>> affine mapping between DARTEL template and MNI template). I
> > > >>>>>>> haven't had a chance to update the user guide for DARTEL yet,
> > > >>>>>>> but it should be reasonably straightforward to use.
> > > >>>>>>>
> > > >>>>>>> I expect that the t stats should be increased, and look forward
> >
> > to
> >
> > > >>>>>>> any feedback on whether this is the case.
> > > >>>>>>>
> > > >>>>>>> Best regards,
> > > >>>>>>> -John
> > > >>>>>>>
> > > >>>>>>> On Tuesday 24 March 2009 16:22, Amir Tahmasebi wrote:
> > > >>>>>>>> Dear John and SPMers,
> > > >>>>>>>>
> > > >>>>>>>> I am trying to use DARTEL for normalization of fMRI data. I
> > > >>>>>>>> have looked at "how to use DARTEL for normalizing fMRI con
> > > >>>>>>>> maps?" thread but it is not exactly what I was looking for.
> > > >>>>>>>>
> > > >>>>>>>> I was wondering how should I use the outputs of DARTEL
> > > >>>>>>>> ("u_rc1*.nii" and "Template_6.nii") to normalize my fMRI data
> > > >>>>>>>> which is already coregistered to the corresponding structural
> > > >>>>>>>> data.
> > > >>>>>>>>
> > > >>>>>>>> Thank you,
> > > >>>>>>>> Amir