<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
<div class="moz-cite-prefix">Hi<br>
<br>
thanks for this clear answer.<br>
<br>
I guess then that a possible improvement would be for the
estimate_response (and csdevonc) programs<br>
to change<br>
<br>
-lmax order set the maximum harmonic order to be estimated. By
default, the<br>
program will use the highest possible lmax given
the number of<br>
diffusion-weighted images.<br>
<br>
by<br>
<br>
<br>
-lmax order set the maximum harmonic order to be estimated. By
default, the<br>
program will use the highest possible lmax given
the number of<br>
<u><i>independant direction</i></u><u>.</u><br>
<br>
Best<br>
<br>
Romain<br>
<br>
Le 07/12/2012 02:47, Robert Smith a écrit :<br>
</div>
<blockquote
cite="mid:CAAVKx7ViMR=swTgM+3X4SeY1buuZfRox9zkcmaDvtSHm8E+kNg@mail.gmail.com"
type="cite">Romain<br>
<br>
The issue here is that estimate_response automatically determines
the maximum harmonic order lmax based on the number of
diffusion-weighted directions it finds in the DWI. In the case of
your data, it finds 60 diffusion-weighted directions, so fits a
spherical harmonic order of 8 (which requires 45 coefficients).
However you only actually have 30 unique directions, with each
acquired twice. So there is only enough angular resolution to fit
a spherical harmonic order of 6 (which requires 28 coefficients).
If you provide the option -lmax 6 to estimate_response, it
calculates a response function similar to those you obtained from
each half-dataset.<br>
<br>
CSD is capable of calculating Fibre Orientation Distributions of a
higher order than you have the data to support ('super-resolved'
CSD), as it incorporates additional information from those
directions where the FOD is negative. You _may_ be able to perform
CSD with an lmax of 8, but it is possible that some voxels will
fail to converge (this will give an error on the command-line, and
the corresponding voxel in your image will be black and contain
NAN values). If this occurs frequently in your images, you will be
limited to using an lmax of 6 for CSD for these data (use "-lmax
6" at the command line for csdeconv).<br>
<br>
Best regards<br>
Rob<br>
<div class="gmail_extra"><br clear="all">
<div><br>
--<br>
<br>
Robert Smith<br>
PhD Candidate <br>
<br>
The Florey Institute of Neuroscience and Mental Health<br>
Melbourne Brain Centre - Austin Campus<br>
245 Burgundy Street<br>
Heidelberg Vic 3084<br>
Ph: +61 3 9035 7128<br>
Fax: +61 3 9035 7301<br>
<a moz-do-not-send="true" href="http://www.florey.edu.au"
target="_blank">www.florey.edu.au</a><br>
<span style="font-size:9pt;font-family:"Times New
Roman","serif";color:red"></span></div>
<br>
<br>
<br>
<div class="gmail_quote">On Wed, Dec 5, 2012 at 2:41 AM, romain
valabregue <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:romain.valabregue@upmc.fr" target="_blank">romain.valabregue@upmc.fr</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear All<br>
<br>
I have an acquisition which has been done with the same
direction twice. (this was an error intead of using a
complementary set of direction it uses the same diffusion
directions)<br>
<br>
when I do the estimate_response on the all data set I get
wrong estimation<br>
<br>
cat response.txt<br>
-4.04413e+15 1.47696e+14 -1.52359e+15 -3.50894e+15
6.85026e+15<br>
<br>
<br>
but when I do the estimation on the half of the dataset
(either the first one or the second one)<br>
I get a correct estimation<br>
<br>
cat response_sh.txt<br>
504.145 -226.698 65.6188 -14.786<br>
cat response_sh2.txt<br>
492.199 -215.285 64.4914 -10.5965<br>
<br>
<br>
Any idea how I can handle the 2 NEX correctly in mrtrix<br>
<br>
<br>
Thanks<br>
<br>
<br>
Romain<br>
<br>
_______________________________________________<br>
Mrtrix-discussion mailing list<br>
<a moz-do-not-send="true"
href="mailto:Mrtrix-discussion@www.nitrc.org"
target="_blank">Mrtrix-discussion@www.nitrc.org</a><br>
<a moz-do-not-send="true"
href="http://www.nitrc.org/mailman/listinfo/mrtrix-discussion"
target="_blank">http://www.nitrc.org/mailman/listinfo/mrtrix-discussion</a><br>
</blockquote>
</div>
<br>
</div>
</blockquote>
<br>
</body>
</html>