Dear Sir,I've used dcm2nii software for conversionOn Fri, Oct 24, 2014 at 5:06 PM, John Ashburner <[log in to unmask]> wrote:The voxel sizes seem to be wrong. I don't know what software you used to do your file conversion, but perhaps you could try the DICOM button of SPM in order to convert from DICOM to NIfTI format.Best regards,-JohnOn 24 October 2014 12:27, Amy R <[log in to unmask]> wrote:Dear Sir,The original image looks like this. (attached)Sorry to say that, we don't have a physicist in our lab to help to deal with these issues.On Thu, Oct 23, 2014 at 4:28 PM, John Ashburner <[log in to unmask]> wrote:I'd suggest taking a look at the original images to see if you have the voxel sizes set correctly. Perhaps your local MR physicists will be able to help here.Best regards,-JohnOn 23 October 2014 04:29, Amy R <[log in to unmask]> wrote:Dear Sir,I made an attempt to do the preprocessing steps without normalization and the image of smoothed image is attached.Can you please tell me, is this the way to get the output?The steps which I followed are Realign – Slice time corr- Coreg- Smoothing..Thanks in advanceOn Fri, Oct 17, 2014 at 12:53 PM, Marko Wilke <[log in to unmask]> wrote: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]tuebingen.de<[log in to unmask]tuebingen.de<mailto:[log in to unmask]tuebingen.de>> 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
<mailto:[log in to unmask]tuebingen.de>
<mailto:[log in to unmask]tuebingen.de________________________________________________________
<mailto:[log in to unmask]tuebingen.de>>> 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
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<mailto:[log in to unmask]tuebingen.de
<mailto:[log in to unmask]tuebingen.de>>
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<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]__de
<mailto:[log in to unmask]tuebingen.de>
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]de
http://www.medizin.uni-tuebingen.de/kinder/epn/
____________________________________________________