<div><div>Dear Mrtrix specialists,</div><div><br></div><div>I am completely new to Mrtrix and am trying to get it to work.</div><div>When doing streamtrack commands however I seem to meet problems.</div><div><br></div><div>
I tried both DT_STREAM and SD_STREAM, bot none of them worked.</div><div><br></div><div>Below please see the error messages.</div><div><br></div><div>I'd like to ask what seems wrong. Is it te tensor image itself? I created it using dwi2tensor form DICOM images.</div>
<div><br></div><div>The CC_mask.nii is a binary mask (1 layer), handdrawn on the corpus callosum.</div><div><br></div><div>Thanks in advance!</div><div>Markus Gschwind</div><div><br></div><div><br></div><div>markus$ streamtrack -debug -info -seed CC_mask.nii DT_STREAM tensor.nii CC_tract</div>
<div><br></div><div>streamtrack [INFO]: opening image "tensor.nii"...</div><div>streamtrack [DEBUG]: preparing file "./tensor.nii"</div><div>streamtrack [DEBUG]: file "./tensor.nii" mapped at 0x101000000, size 16908640 (read-only)</div>
<div>streamtrack [DEBUG]: sanitising transformation matrix...</div><div>streamtrack [DEBUG]: unmapping file "./tensor.nii"</div><div>streamtrack [DEBUG]: setting up image "tensor.nii"...</div><div>streamtrack [DEBUG]: sanitising transformation matrix...</div>
<div>streamtrack [DEBUG]: setting up data increments for "tensor.nii"...</div><div>streamtrack [DEBUG]: data increments initialised with start = 0, stride = [ 1 128 16384 704512 ]</div><div>streamtrack [INFO]: error parsing spherical ROI specification "CC_mask.nii" - assuming mask image</div>
<div>streamtrack [DEBUG]: mapping image "tensor.nii"...</div><div>streamtrack [DEBUG]: file "./tensor.nii" mapped at 0x101000000, size 16908640 (read-only)</div><div>streamtrack [DEBUG]: data mapper for image "tensor.nii" mapped with segment size = 4227072 (optimised)</div>
<div>streamtrack [INFO]: launching 1 threads</div><div>streamtrack [INFO]: found 0x0 diffusion-weighted encoding</div><div>streamtrack: invalid gradient matrix dimensions</div><div>streamtrack [INFO]: closing image "tensor.nii"...</div>
<div>streamtrack [DEBUG]: unmapping file "./tensor.nii"</div></div><div><br></div><div><br></div><div><br></div><div><br></div><div><div>Markus-Gschwinds-MacBook-Pro:Case_SSS markus$ streamtrack -debug -info -seed CC_mask.nii SD_STREAM tensor.nii CC_tract</div>
<div><br></div><div>streamtrack [INFO]: opening image "tensor.nii"...</div><div>streamtrack [DEBUG]: preparing file "./tensor.nii"</div><div>streamtrack [DEBUG]: file "./tensor.nii" mapped at 0x101000000, size 16908640 (read-only)</div>
<div>streamtrack [DEBUG]: sanitising transformation matrix...</div><div>streamtrack [DEBUG]: unmapping file "./tensor.nii"</div><div>streamtrack [DEBUG]: setting up image "tensor.nii"...</div><div>streamtrack [DEBUG]: sanitising transformation matrix...</div>
<div>streamtrack [DEBUG]: setting up data increments for "tensor.nii"...</div><div>streamtrack [DEBUG]: data increments initialised with start = 0, stride = [ 1 128 16384 704512 ]</div><div>streamtrack [INFO]: error parsing spherical ROI specification "CC_mask.nii" - assuming mask image</div>
<div>streamtrack [DEBUG]: mapping image "tensor.nii"...</div><div>streamtrack [DEBUG]: file "./tensor.nii" mapped at 0x101000000, size 16908640 (read-only)</div><div>streamtrack [DEBUG]: data mapper for image "tensor.nii" mapped with segment size = 4227072 (optimised)</div>
<div>streamtrack [INFO]: launching 1 threads</div><div>streamtrack [INFO]: opening image "CC_mask.nii"...</div><div>streamtrack [DEBUG]: preparing file "./CC_mask.nii"</div><div>streamtrack [DEBUG]: file "./CC_mask.nii" mapped at 0x102021000, size 1409376 (read-only)</div>
<div>streamtrack [DEBUG]: sanitising transformation matrix...</div><div>streamtrack [DEBUG]: unmapping file "./CC_mask.nii"</div><div>streamtrack [DEBUG]: setting up image "CC_mask.nii"...</div><div>streamtrack [DEBUG]: sanitising transformation matrix...</div>
<div>streamtrack [DEBUG]: setting up data increments for "CC_mask.nii"...</div><div>streamtrack [DEBUG]: data increments initialised with start = 0, stride = [ 1 128 16384 ]</div><div>streamtrack [DEBUG]: mapping image "CC_mask.nii"...</div>
<div>streamtrack [DEBUG]: file "./CC_mask.nii" mapped at 0x102021000, size 1409376 (read-only)</div><div>streamtrack [DEBUG]: data mapper for image "CC_mask.nii" mapped with segment size = 704512</div>
<div>streamtrack [INFO]: failed to find SH peak!</div><div>streamtrack [INFO]: failed to find SH peak!</div><div>streamtrack [INFO]: failed to find SH peak!</div><div>streamtrack [INFO]: failed to find SH peak!</div><div>
streamtrack [INFO]: failed to find SH peak!</div><div>streamtrack [INFO]: failed to find SH peak!</div><div>streamtrack [INFO]: failed to find SH peak!</div><div>streamtrack [INFO]: failed to find SH peak!</div><div>streamtrack [INFO]: failed to find SH peak!</div>
<div>streamtrack [INFO]: failed to find SH peak!</div></div><div><br></div><div><br></div><div><br></div>-- <br><br><br>