Amy,
> *of T1W images (actually..it's an optional step, which I do fr my
> subjects to get bias corrected images..)*
That wold indeed be optional for your fMRI processing stream (except for
generating spatial normalization parameters for later spatial
normalization).
> *Okay.. I understand the need for omission to get that in native
> form...Thanks*
You don't need to do anything to get your subjects into your subject's
native space. This is how the data is acquired.
> *So here... If I take my T1W image as /reference image /and /source
> image/ as mean of EPI scans..and /other images/ as unwarped images...
> will that be correct Marko??*
You can move that anatomical to the space of the EPIs, or you can move
the EPIs to the space of the anatomical. Either way should work,
although I also prefer the latter. What you described should work.
> *Here again I have a doubt, ...as this pertains to fMRI scans...we get
> con images only after preprocessing steps right?? To be more clear...
> only after preproc..I can do first level right...*
Preprocessing is what comes before single subject statistical analyses.
The point you initially asked is, does spatial normalization have to be
part of preprocessing. The answer (well, my answer) was no, you can
perform spatial normalization after single subject statistical analysis.
Within spm, con-images are resulting from setting up a statistical
analysis and then generating a contrast (hence the name). These are
usually taken to group analyses. However, all of this depends very much
on your analysis approach, which is up to you to decide.
Cheers,
Marko
>
> 6.Smooth
>
>
> Yes.
>
> What changes needs to be done in my preprocessing steps...
> I actually want to do fmRI MRS correlation,.
>
>
> In that case you may want to optimize your processing for resting state
> processing in any case, see the several hundred papers addressing this,
> as well as the toolboxes specifically designed for this purpose*.**
>
>
> Okay..*
>
> I am attaching a paper where they used native space processing for
> that...
> Please go thru the page no. 4 of this article
> and kindly let me knw how to do it...
>
>
> No. You asked me a question to which I gave you an answer (or rather, an
> opinion), in the hope that it would be helpful. I am not going to go
> through papers with you.
>
> *That's perfect. No issues. Thanks for helping me in clarify the doubts..*
>
> On Fri, Oct 17, 2014 at 12:13 PM, Marko Wilke
> <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> Amy,
>
> So...before considering the first level, I like statr from the
> beginning.
> Say from preprocessing step...
>
>
> Yes, that makes sense :)
>
> Usually, the steps which I perform are
> 1. Segmentation
>
>
> ... of what?
>
> 2. Normalize: Write (This actually takes ur template to MNI which I
> don't want... So how to handle this step?)
>
>
> ... as I said, omit it here. Not sure what you mean by "template to
> MNI space" as usually a template is in normalized (e.g., MNI) space
> to begin with.
>
> 3. ReALIGN ANd unwarp
>
>
> ... which I would do in native space anyway.
>
> 4. Coregistration: Estimate
>
>
> ... you can happily do that in native space, too.
>
> 5. Normalize:Write
>
>
> ... again? I guess this pertains to the functional images. In this
> case, you would probably select the con-images from your first level
> statistics.
>
> 6.Smooth
>
>
> Yes.
>
> What changes needs to be done in my preprocessing steps...
> I actually want to do fmRI MRS correlation,.
>
>
> In that case you may want to optimize your processing for resting
> state processing in any case, see the several hundred papers
> addressing this, as well as the toolboxes specifically designed for
> this purpose.
>
> I am attaching a paper where they used native space processing
> for that...
> Please go thru the page no. 4 of this article
> and kindly let me knw how to do it...
>
>
> No. You asked me a question to which I gave you an answer (or
> rather, an opinion), in the hope that it would be helpful. I am not
> going to go through papers with you.
>
> Cheers,
> Marko
>
>
> On Fri, Oct 17, 2014 at 11:41 AM, Marko Wilke
> <[log in to unmask]
> <mailto:[log in to unmask]>
> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>>> wrote:
>
> Hi Amy,
>
> I'd like to do an fMRI experiment wherein, instead of
> taking the
> subject template to MNI template, I need them in their
> native
> space. MAy
> I know how to perform such experiment?
>
>
> This will actually be easier on the first level as you
> simply skip
> the step of spatial normalization :) It becomes slightly
> more tricky
> afterwards but not overly so: instead of normalizing all
> EPI images,
> you now only normalize the con-images and perform second-level
> statistics on these. One issue to be aware of is that more
> extensive
> interpolation schemes (such as higher level b-splines in
> spm) will
> lead to out-of-brain voxels not being absolutely 0, which may
> interfere with mask generation. You can use an explicit
> mask to that
> effect.
>
> Incidentally, I think this is actually the preferred approach:
> mathematically, they should yield pretty much equivalent
> results but
> they don't. The issue, of course, is interpolation, and without
> having explored this exhaustively, I believe that one can
> make the
> case that it is better "to interpolate" the results
> (generated from
> non-interpolated raw data) than "to interpolate" the raw
> data. But
> that is only my 2 cents.
>
> Cheers,
> Marko
>
> --
> ________________________________________________________
> PD Dr. med. Marko Wilke
> Facharzt für Kinder- und Jugendmedizin
> Leiter, Experimentelle Pädiatrische Neurobildgebung
> Universitäts-Kinderklinik
> Abt. III (Neuropädiatrie)
>
> Marko Wilke, MD, PhD
> Pediatrician
> Head, Experimental Pediatric Neuroimaging
> University Children's Hospital
> Dept. III (Pediatric Neurology)
>
> Hoppe-Seyler-Str. 1
> D - 72076 Tübingen, Germany
> Tel. +49 7071 29-83416
> Fax +49 7071 29-5473
> [log in to unmask]
> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>>
>
> http://www.medizin.uni-____tuebingen.de/kinder/epn/
> <http://www.medizin.uni-__tuebingen.de/kinder/epn/>
> <http://www.medizin.uni-__tuebingen.de/kinder/epn/
> <http://www.medizin.uni-tuebingen.de/kinder/epn/>>
> ________________________________________________________
>
>
>
> --
> ______________________________________________________
> PD Dr. med. Marko Wilke
> Facharzt für Kinder- und Jugendmedizin
> Leiter, Experimentelle Pädiatrische Neurobildgebung
> Universitäts-Kinderklinik
> Abt. III (Neuropädiatrie)
>
> Marko Wilke, MD, PhD
> Pediatrician
> Head, Experimental Pediatric Neuroimaging
> University Children's Hospital
> Dept. III (Pediatric Neurology)
>
> Hoppe-Seyler-Str. 1
> D - 72076 Tübingen, Germany
> Tel. +49 7071 29-83416
> Fax +49 7071 29-5473
> [log in to unmask]
> <mailto:[log in to unmask]>
>
> http://www.medizin.uni-__tuebingen.de/kinder/epn/
> <http://www.medizin.uni-tuebingen.de/kinder/epn/>
> ______________________________________________________
>
>
--
____________________________________________________
PD Dr. med. Marko Wilke
Facharzt für Kinder- und Jugendmedizin
Leiter, Experimentelle Pädiatrische Neurobildgebung
Universitäts-Kinderklinik
Abt. III (Neuropädiatrie)
Marko Wilke, MD, PhD
Pediatrician
Head, Experimental Pediatric Neuroimaging
University Children's Hospital
Dept. III (Pediatric Neurology)
Hoppe-Seyler-Str. 1
D - 72076 Tübingen, Germany
Tel. +49 7071 29-83416
Fax +49 7071 29-5473
[log in to unmask]
http://www.medizin.uni-tuebingen.de/kinder/epn/
____________________________________________________
|