[Camino-users] Bfloat to Matlab

[Perea Camargo, Rodrigo Dennis]

Hi Mahmoud,
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).
The function to read these tracts is here: https://github.com/Drigomaniac/rotrk_landmarks/blob/master/rotrk_read.m
The Information was extracted from: http://www.trackvis.org/docs/?subsect=fileformat
Hope this helps,
Rodrigo


From: <camino-users-bounces at www.nitrc.org> on behalf of Mahmoud <zeydabadi at gmail.com>
Date: Monday, November 13, 2017 at 11:06 AM
To: "camino-users at www.nitrc.org" <camino-users at www.nitrc.org>
Subject: [Camino-users] Bfloat to Matlab

Hello all,

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.

fslmaths  $1/$sub/data/data_FA.nii.gz -thr 0.3 -bin $1/$sub/tract/data_FA_thr03.nii.gz
cp $1/$sub/data/nodif_brain_mask_trimmed.nii.gz $1/$sub/tract/nodif_brain_mask_trimmed.nii.gz
TVFromEigenSystem -basename $1/$sub/data/data -type FSL -out $1/$sub/tract/data_tensor.nii.gz
/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
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
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

Thank you!
Mahmoud


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