[Mristudio-users] diffeomap Byte conversion problems

[susumu mori]

Hi Maheen,

You said that you are running the single-channel LDDMM. That means you need
to submit only one atlas image and one subject image. So, you don't need all
FA, b0, and *.d. You have to pick one. After LDDMM, you will receive
transformation matrices. You can apply these matrices to any maps
co-registered to the one you picked to drive the registration. For DTI, we
recommend two-channel LDDMM using b0+FA or Trace+FA. In this case, you have
to convert to byte both images.

This process is explained in "Getting Started" section of
https://www.mristudio.org/wiki/user_manual/diffeomap.

As for the byte conversion, please make sure that you converted both
template and subject images.

If you have repeated b0, your table should look like;

1: 0, 0, 0
2: 0, 0, 0
3: 0, 0, 0
4: 1, 0, 0
and so on, if you have three repeated b0s.

Susumu

On Fri, Aug 27, 2010 at 6:00 PM, Maheen M. Adamson <madamson at stanford.edu>wrote:

> Hello,
>
>
>
> There are a few questions we have as we run through the sample data for
> Diffeomap. We are trying to send the preprocessed sample data through to
> single channel LDDMM server. We have subject_AIR_FA, subject_AIR_b0 and
> Subject_AIR_d. We used the small button to change the file format to byte,
> saved it as Image_Byte_Subject_Air. But every time we hit the send to
> server
> button, we get the complaint that the image is not a byte image. It is also
> complaining that the template has to be binary (which is the atlas_MN_SS
> file).
>
>
>
> Also, can you also tell us how to deal with repeat gradients (B0 appears
> three times when you do repeat gradient tables)? Do we just paste the
> gradient table (with repeats)? Keeps asking me if I want to forget the B0
> field.
>
>
>
> Thank you
>
> Maheen
>
>
>
> Maheen Mausoof Adamson, PhD
>
>
>
> Clinical Assistant Professor (affiliated)
>
> Psychiatry & Behavioral Sciences
>
> Stanford School of Medicine
>
> Stanford CA
>
>
>
> Director of Clinical Neuroscience
>
> Deputy Director, Data core
>
> War Related Illness and Injury Study Center (WRIISC)
>
> Vetarans Affairs, Palo Alto Health Care System
>
> Palo Alto, CA
>
> Phone: (650) 493-5000 x62179
>
> Fax: (650) 852-3297
>
> Email: madamson at stanford.edu
>
> maheen.adamson at va.gov
>
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