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<p class="MsoNormal">Hi Mahmoud, <o:p></o:p></p>
<p class="MsoNormal">In case this helps, I am currently working on some of these tools to read *.trk and *.trk.gz files in matlab (coming from trackvis/dsi_studio, it will be interesting to see if they also work with camino output).<o:p></o:p></p>
<p class="MsoNormal">The function to read these tracts is here: <a href="https://github.com/Drigomaniac/rotrk_landmarks/blob/master/rotrk_read.m">
https://github.com/Drigomaniac/rotrk_landmarks/blob/master/rotrk_read.m</a> <o:p>
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<p class="MsoNormal">The Information was extracted from: <a href="http://www.trackvis.org/docs/?subsect=fileformat">
http://www.trackvis.org/docs/?subsect=fileformat</a><o:p></o:p></p>
<p class="MsoNormal">Hope this helps, <o:p></o:p></p>
<p class="MsoNormal">Rodrigo<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black"><camino-users-bounces@www.nitrc.org> on behalf of Mahmoud <zeydabadi@gmail.com><br>
<b>Date: </b>Monday, November 13, 2017 at 11:06 AM<br>
<b>To: </b>"camino-users@www.nitrc.org" <camino-users@www.nitrc.org><br>
<b>Subject: </b>[Camino-users] Bfloat to Matlab<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hello all,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I used the following commands to do tractography with camino. Could someone please let me know whether I did it right and if it's correct how can I read that bfloat file in MATLAB? My goal is to have the coordinate of fiber tracts in MATLAB.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><i>fslmaths $1/$sub/data/data_FA.nii.gz -thr 0.3 -bin $1/$sub/tract/data_FA_thr03.nii.gz</i></b><o:p></o:p></p>
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<p class="MsoNormal"><b><i>cp $1/$sub/data/nodif_brain_mask_trimmed.nii.gz $1/$sub/tract/nodif_brain_mask_trimmed.nii.gz</i></b><o:p></o:p></p>
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<p class="MsoNormal"><b><i>TVFromEigenSystem -basename $1/$sub/data/data -type FSL -out $1/$sub/tract/data_tensor.nii.gz</i></b><o:p></o:p></p>
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<p class="MsoNormal"><b><i>/camino/bin/nii2dt -inputfile $1/$sub/tract/data_tensor.nii.gz -bgmask $1/$sub/tract/nodif_brain_mask_trimmed.nii.gz -uppertriangular > $1/$sub/tract/tensor.Bdouble</i></b><o:p></o:p></p>
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<p class="MsoNormal"><b><i>cat $1/$sub/tract/tensor.Bdouble | track -inputmodel dt -seedfile $1/$sub/tract/data_FA_thr03.nii.gz -outputroot $1/$sub/tract/WB_one_tensor -curvethresh 80 -anisthresh 0.3</i></b><o:p></o:p></p>
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<p class="MsoNormal"><b><i>camino_to_trackvis -i $1/$sub/tract/WB_one_tensor1.Bfloat -o $1/$sub/tract/WB_one_tensor.trk --nifti $1/$sub/tract/nodif_brain_mask_trimmed.nii.gz --phys-coords</i></b><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Thank you!<o:p></o:p></p>
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<p class="MsoNormal">Mahmoud<o:p></o:p></p>
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