Hi Maheen,<br><br>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.<br>
<br>This process is explained in "Getting Started" section of <a href="https://www.mristudio.org/wiki/user_manual/diffeomap">https://www.mristudio.org/wiki/user_manual/diffeomap</a>.<br><br>As for the byte conversion, please make sure that you converted both template and subject images.<br>
<br>If you have repeated b0, your table should look like;<br><br>1: 0, 0, 0<br>2: 0, 0, 0<br>3: 0, 0, 0<br>4: 1, 0, 0<br>and so on, if you have three repeated b0s.<br><br>Susumu<br><br><div class="gmail_quote">On Fri, Aug 27, 2010 at 6:00 PM, Maheen M. Adamson <span dir="ltr"><<a href="mailto:madamson@stanford.edu">madamson@stanford.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Hello,<br>
<br>
<br>
<br>
There are a few questions we have as we run through the sample data for<br>
Diffeomap. We are trying to send the preprocessed sample data through to<br>
single channel LDDMM server. We have subject_AIR_FA, subject_AIR_b0 and<br>
Subject_AIR_d. We used the small button to change the file format to byte,<br>
saved it as Image_Byte_Subject_Air. But every time we hit the send to server<br>
button, we get the complaint that the image is not a byte image. It is also<br>
complaining that the template has to be binary (which is the atlas_MN_SS<br>
file).<br>
<br>
<br>
<br>
Also, can you also tell us how to deal with repeat gradients (B0 appears<br>
three times when you do repeat gradient tables)? Do we just paste the<br>
gradient table (with repeats)? Keeps asking me if I want to forget the B0<br>
field.<br>
<br>
<br>
<br>
Thank you<br>
<br>
Maheen<br>
<br>
<br>
<br>
Maheen Mausoof Adamson, PhD<br>
<br>
<br>
<br>
Clinical Assistant Professor (affiliated)<br>
<br>
Psychiatry & Behavioral Sciences<br>
<br>
Stanford School of Medicine<br>
<br>
Stanford CA<br>
<br>
<br>
<br>
Director of Clinical Neuroscience<br>
<br>
Deputy Director, Data core<br>
<br>
War Related Illness and Injury Study Center (WRIISC)<br>
<br>
Vetarans Affairs, Palo Alto Health Care System<br>
<br>
Palo Alto, CA<br>
<br>
Phone: (650) 493-5000 x62179<br>
<br>
Fax: (650) 852-3297<br>
<br>
Email: <a href="mailto:madamson@stanford.edu">madamson@stanford.edu</a><br>
<br>
<a href="mailto:maheen.adamson@va.gov">maheen.adamson@va.gov</a><br>
<br>
NOTICE: DO NOT SEND ME ANY FORM OF PROTECTED HEALTH INFORMATION (PHI) UNDER<br>
ANY CIRCUMSTANCES.<br>
<br>
<br>
<br>
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<br></blockquote></div><br>