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Thanks Rodrigo.
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<div class="">I don't know much about TrackVis but the Camino streamline format is documented here:</div>
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<div class=""><a href="http://camino.cs.ucl.ac.uk/index.php?n=Main.Fileformats#toc11" class="">http://camino.cs.ucl.ac.uk/index.php?n=Main.Fileformats#toc11</a></div>
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<div class="">It's big-endian, 32-bit floats, which should be readable directly into Matlab if needed. You need to read them iteratively. The first value tells you how many points follow. The next is an integer index (but still stored as float) indicating which
point is the seed point. Then the points themselves follow. Repeat until EOF.</div>
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<div class="">On Nov 13, 2017, at 11:14 AM, Perea Camargo, Rodrigo Dennis <<a href="mailto:RPEREACAMARGO@mgh.harvard.edu" class="">RPEREACAMARGO@mgh.harvard.edu</a>> wrote:</div>
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Hi Mahmoud,<span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
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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 class=""></o:p></div>
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The function to read these tracts is here:<span class="Apple-converted-space"> </span><a href="https://github.com/Drigomaniac/rotrk_landmarks/blob/master/rotrk_read.m" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">https://github.com/Drigomaniac/rotrk_landmarks/blob/master/rotrk_read.m</a><o:p class=""></o:p></div>
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The Information was extracted from:<span class="Apple-converted-space"> </span><a href="http://www.trackvis.org/docs/?subsect=fileformat" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">http://www.trackvis.org/docs/?subsect=fileformat</a><o:p class=""></o:p></div>
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Hope this helps,<span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
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Rodrigo<o:p class=""></o:p></div>
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<b class=""><span style="font-size: 12pt;" class="">From:<span class="Apple-converted-space"> </span></span></b><span style="font-size: 12pt;" class=""><<a href="mailto:camino-users-bounces@www.nitrc.org" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">camino-users-bounces@www.nitrc.org</a>>
on behalf of Mahmoud <<a href="mailto:zeydabadi@gmail.com" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">zeydabadi@gmail.com</a>><br class="">
<b class="">Date:<span class="Apple-converted-space"> </span></b>Monday, November 13, 2017 at 11:06 AM<br class="">
<b class="">To:<span class="Apple-converted-space"> </span></b>"<a href="mailto:camino-users@www.nitrc.org" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">camino-users@www.nitrc.org</a>" <<a href="mailto:camino-users@www.nitrc.org" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">camino-users@www.nitrc.org</a>><br class="">
<b class="">Subject:<span class="Apple-converted-space"> </span></b>[Camino-users] Bfloat to Matlab<o:p class=""></o:p></span></div>
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Hello all,<o:p class=""></o:p></div>
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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 class=""></o:p></div>
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<b class=""><i class="">fslmaths $1/$sub/data/data_FA.nii.gz -thr 0.3 -bin $1/$sub/tract/data_FA_thr03.nii.gz</i></b><o:p class=""></o:p></div>
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<b class=""><i class="">cp $1/$sub/data/nodif_brain_mask_trimmed.nii.gz $1/$sub/tract/nodif_brain_mask_trimmed.nii.gz</i></b><o:p class=""></o:p></div>
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<b class=""><i class="">TVFromEigenSystem -basename $1/$sub/data/data -type FSL -out $1/$sub/tract/data_tensor.nii.gz</i></b><o:p class=""></o:p></div>
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<b class=""><i class="">/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 class=""></o:p></div>
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<b class=""><i class="">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 class=""></o:p></div>
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<b class=""><i class="">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 class=""></o:p></div>
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Thank you!<o:p class=""></o:p></div>
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Mahmoud<o:p class=""></o:p></div>
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