[Camino-users] Need help with an issue using qball reconstruction

[Parvathaneni, Prasanna]

Hi,

   We are trying to use the qball reconstruction as indicated in the tutorial for squirrel monkey data set whose scheme file is as attached. Its dimensions are 128X192X96.

We are having issues viewing the rgb file that is generated as below after running sfplot on split files. Below are more details related to this issue.



  *   The exact commands that produce the problem.

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#qballmx -schemefile data1.scheme > qballMatrix_data1.Bdouble

#linrecon dwi_data1.Bfloat data1.scheme  qballMatrix_data1.Bdouble -normalize -bgmask  brain_mask.nii.gz > dwi_ODF_data1.Bdouble
#split -b $((128*192*248*8))  dwi_ODF_data1.Bdouble ./splitBrain/dwi_ODFs_data1_slice
#split -b $((128*192*8))  fa_data1.img  ./splitBrain/fa_data1_slice
#sfplot -inputmodel rbf -rbfpointset 246 -rbfsigma 0.2618 -xsize 128 -ysize 192 -minifigsize 10 10 -minifigseparation 2 2 -minmaxnorm -dircolcode -projection 1 -2 -backdrop ./splitBrain/fa_data1_slicebr < ./splitBrain/dwi_ODFs_data1_slicear > dwi_ODFs_slicear.rgb

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MATLAB script for loading and viewing the rgb file.

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fid = fopen('dwi_ODFs_slicear.rgb','r','b');
dwiODFs = fread(fid,'unsigned char');
fclose(fid);
imageODFs = reshape(dwiODFs,3,6144,4096); % Image size obtained from camino output
imageODFs = uint8(permute(imageODFs,[2 3 1]));
imshow(imageODFs,[]);
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  *   Attached is the scheme file (data1.scheme)
  *   Attached is the output given out when running qball commands  (qballoutput.txt)



  *   Any error messages that result.

  *   Attached is the info message when opening the rgb file from MATLAB. (Qball_ImageView_Issues.JPG)
  *   Also Attached is the image file that is displayed (QBall_sliceview_Issues.JPG)

Can you please assist.



Thanks,

Prasanna
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