[Mristudio-users] How to combine DTI data from different runs

[Darren Gitelman]

Dear Susumu

Thanks for the speedy reply. Regarding the 2 issues you mentioned

> 1) You can specify the number of signal averaging in Siemens. I'm not sure
> why you thought you couldn't. However, if you meant, "Siemens saved all
> images separately without averaging", then you are correct.

Our physicist said for this particular sequence repeats were not
possible. He is not sure why and also seemed surprised that the choice
was grayed out.

> 2) DtiStudio can read repeated scans and combine them for one DTI
> calculation.

Excellent. So the next question is how to do this? I read through the
manual, but I did not see where this type of calculation was
specified.

- I loaded all 3 repeated scans by adding the folders to the Dicom
Image File Folders, and all the scans loaded properly.
- My guess is the next step is to realign all the images using AIR. I
have a couple of questions about this.
   - What is the optional upper bound?
   - Which cost function is best to use?
   - Should I adjust the gradients for the diffusion weighted images?

- Once Air finishes I have a bunch of images labeled Air-series-blah\
-1, Air-series-blah\ -2, etc.
  - How do I save these images so I can just reload them later and not
have to redo-air.
  - How do I get DTI studio to use these images rather than the
original images for the FA calculation?
  - How do I tell DTIstudio to combine the images across the repeats?

Thanks again,
Darren



> Hi Darren,
>
> In a previous communication in the mailing list, I explained why we can not
> use regular k-space averaging for DTI and, therefore, we average data after
> magnitude calculation (we average images, not k-space data). If anybody
> remembers which thread it was, I would appreciate it.
>
> Anyway, because we first have to calculate image before averaging, there is
> no point to ask scanners to do the averaging. One downside of the
> averaging-by-the-scanner is, if the images are mis-registered or there are
> corrupted images, we can not undo the averaging.
>
> I believe that is why Siemens always save all images separately (without
> creating an "averaged image" even if multiple averaging is specified.
>
> Please note the difference between "repeated scans (you submitted the same
> protocol twice)" and "averaged scans (you specified 2 signal averaging)"
> when you use Siemens. Either way, all images are saved individually and they
> are basically the same studies. However, in the former case, the "repeated
> images" are stored in different directories and Siemens console can not
> combine them for DTI  calculation. With the latter case, the repeated images
> are stored in the same directory and Siemens console can combine them to
> calculate one DTI data.
>
> Either way, when you use DtiStudio, you need to load all files at once and
> DtiStudio can combine them to calculate one DTI.
>
> Now going back to your question;
>
> 1) You can specify the number of signal averaging in Siemens. I'm not sure
> why you thought you couldn't. However, if you meant, "Siemens saved all
> images separately without averaging", then you are correct.
> 2) DtiStudio can read repeated scans and combine them for one DTI
> calculation.
>
> On Sun, Feb 28, 2010 at 7:54 PM, Darren Gitelman <
> d-gitelman at northwestern.edu> wrote:
>
> > Hello:
> >
> > Is there a way to combine data across several repeats of a DTI sequence?
> >
> > The reason I ask is that we have a Siemens Trio scanner but are
> > working with another group that has a GE scanner. On the GE scanner
> > the DTI sequence allows NEX > 1 (they are getting 4), which appears to
> > improve their SNR considerably. The Siemens sequences do not allow
> > this, so we are repeating the DTI sequence several times, and want to
> > combine the data across runs. Can this be done within DTIstudio or
> > some other program? Would it be best to do this at the level of the
> > DTI images or the FA maps?
> >
> > Thanks,
> > Darren