<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:verdana,helvetica,sans-serif;font-size:10pt">Hello to all mrtrix users and developers :) <br><br>I am new to mrtrix and trying to tune some parameters for my data. here my very basic questions. <br><br>(1). <br>This is suggested in the mrtrix docs ''''
The first value should be positive, and have an amplitude similar to the <i>b</i>=0 brain white matter signal
(you can verify this by loading the <kbd>dwi.mif</kbd> image and placing the focus within a white matter region -
the intensity is displaced in the bottom right of the statusbar )''' <br><br>So, when I go to white matter than I found some places 146, 157, 99, 148 and it varies around 100 to 180, just I checked on few places. <br><br>So, when I estimated response for 126 direction dataset, using -lmax 10, 12, 14, I found very minor change between all the resulted response.txt. and the first value of response.txt was higher than the white matter value of my data. <br><br>>estimate_response dwi.mif sf_th0_6.mif -lmax 10 response_sf_th0_6.txt -grad encoding.b <br><br>response text file looks like this. <br>172.802 -82.9005 38.419 -12.4871 2.83802 -0.640453 <br><br>172 is bit higher with the white matter values of my data, so I tried with lmax 14 and lower and looked at the respone text, for example with lmax 14 it has minor change. <br><br>172.655 -83.0056 38.5118 -12.6871 2.58813 -0.679325 0.196577 -0.126814 <br><br><br>So, I looked up and checked the sf.mif ( Mask
of single-fibre voxels ),
and I found it has few voxels only. (also in the site written a mask
containing a few hundred voxels ). I created it at FA = 0.6 threshold.
<br>
see attached with the email (sf_th0_6.mif). <br><br>than I lowered down the threshold to 0.4 (sf_th0_4.mif), and estimated response again (lmax10)<br>159.062 -64.3264 26.9399 -8.18025 1.79083 -0.315482 <br><br>sf_th0_2.mif (0.2 threshold) + lmax10 > response.txt<br>131.734 -36.8685 13.1795 -3.64864 0.777517 -0.140337 <br><br><br>sf_th0_1.mif ( 0.1 threshold ) + lmax12 > response.txt<br>124.456 -26.1018 8.307 -2.14918 0.443511 -0.0872688 <br><br>so, 124.456 was nearer than other response.txt, So, I took this one and performed CSD with lmax12<br>now when I overly odf, than three pictures have some thing else than normal (attached with email). <br><br>I think this was not a good idea to go to sf.mif threshold 0.1. <br><br>So the question is how I can get the best response.txt when data has different white matter values, and the output of response estimate is higher than the lowest value of white matter ?. <br><br><br>(2). Is there any sample dataset,
which fits on the help file standard parametes, so that one could get an idea, how the output should look like for his data also. <br><br>(3). I preprocess data using FSL (eddy current correction) and after that I took them out in .nii format and used LONI debeller for analyze conversion. and later on used mrconvert, and converted in .mif. <br>I think this is okay, if some one have any better way for importing nifti data, let me know.<br><br>thanx <br>vinod<br><br></div><br>
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