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<p class="MsoNormal">Hi,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I have not looked at the code in a long time, but I don't think you need `-header` at all in this case. You just need the bedpost input dir (which contains NIFTI files) and the seed file (which is also NIFTI).<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The seed file should be aligned in physical space with the bedpostx data. If you load one of the 3D bedpost images (eg, mean_f50samples.nii.gz) and overlay the seed image wm_interpolated.nii.gz, they should be aligned. You can do this in
fsleyes or ITK-SNAP.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Regarding the density of the streamlines, aligning the seed regions to the data correctly will likely help. -iterations will start more processes from each voxel center but it might not match what MRtrix or other software does. There's
just a bunch of implementation choices that can affect results, and that's before you even get into the underlying model fits that provide the vector field for the tracking.
<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" style="margin-bottom:12.0pt"><b><span style="font-size:12.0pt;color:black">From:
</span></b><span style="font-size:12.0pt;color:black">Camino-users <camino-users-bounces@www.nitrc.org> on behalf of Sergio II Ramirez <sergioir@uci.edu><br>
<b>Date: </b>Monday, April 5, 2021 at 6:50 PM<br>
<b>To: </b>camino-users@www.nitrc.org <camino-users@www.nitrc.org><br>
<b>Subject: </b>[External] [Camino-users] Track Images Not Aligned<o:p></o:p></span></p>
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<p class="MsoNormal">Hello,<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'm a research assistant who has been running into some issues as of late using Camino's 'track' command and have been at a loss at how to proceed, hoping I can get the help needed here! Apologies if I'm not as well-versed in the field
as others here.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">My exact input is shown below:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">track -bedpostxdir bedpostx.bedpostX -inputmodel bedpostx_dyad -curvethresh 75 -tracker euler -stepsize 0.5 -seedfile wm_interpolated.nii.gz -header wm_LR_bin.nii.gz -outputfile header_test.Bdouble<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Whilst encountering errors such as these shown below:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">WARNING: Seed point<br>
Point3D: (249.5078125, 140.5078125, 50.15000140666961)<br>
is outside the diffusion image space, ignoring<br>
Processing seed 36281 of 4409289Apr 05, 2021 3:07:34 PM apps.StreamlineTractography execute<br>
WARNING: Seed point<br>
Point3D: (251.2109375, 140.5078125, 50.15000140666962)<br>
is outside the diffusion image space, ignoring<br>
Processing seed 36282 of 4409289Apr 05, 2021 3:07:34 PM apps.StreamlineTractography execute<br>
.<o:p></o:p></p>
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<p class="MsoNormal">.<o:p></o:p></p>
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<p class="MsoNormal">.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">We're under the assumption that the two images supplied for the '-header' and '-seedfile' are not aligned properly, even though they both derive from the same dwi, and any attempts to edit the header for either file to align them have not
provided any changes. If it brings any clarification, we utilized FSL in order to create the 'wm_interpolated.nii.gz' file supplied, but again still deriving from the same dwi as before.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Might there be any way to align these two files properly that I am unaware of? Or are we wrong in our assumption and there seems to be a different problem at hand? I would greatly appreciate any help on how to progress.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">As a side note, from the results I have gathered using the command above they seem to be lacking a substantial amount of streamlines as opposed to a colleague of mine who is receiving a larger amount from MRtrix. I'm unsure if the '-iterations'
input is the appropriate method to solving this predicament, and would appreciate any help on this matter as well.<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 for any help that you can provide in my case, it will surely help the studies we are performing here.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Best Regards,<o:p></o:p></p>
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<p class="MsoNormal">Sergio Ramirez II<o:p></o:p></p>
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