Re: [Freesurfer] Tracula with multi-shell data?
Hi Henrik - There's no explicit parameter in the current version, but you can run bedpostx the multi-exponential model yourself, and then let tracula use the orientation estimates from that model (as long as the output dir is called dmri.bedpostX, it'll read the files from there). We are in the process of evaluting this with tracula, but note that I suspect that the benefits for tracula may be limited. The general benefit of the multi-exponential model in bedpostx is that it may produce fewer spurious secondary "sticks" (fiber populations) that you might get when fitting the mono-exponential model of bedpostx to multi-shell DWI data. An exploratory (local) tractography method will follow those spurious orientations and end up in the wrong place. But tracula is a global tractography method, i.e., it fits the pathway to the diffusion orientations everywhere along the pathway, rather at one voxel at a time. So spurious secondary orientations in some of those voxels may not have such a big effect on the final result, hence removing those spurious secondary orientations may not make a big difference. Best, a.y On Wed, 14 Oct 2015, Henrik Sjöström wrote: Hi! I have some questions regarding Tracula and multi-shell DWI. -Is it possible to activate the multi-shell model within bedpostx when running it through tracula? -does anyone have experience on running multi-shell data through Tracula (2 or 3 crossing fibers)? We are planning an experiment and discussing protocols consisting of around 32 directions with b=1000 and 64 directions at b=2500 so I'm looking for opinions on this with regard to Tracula processing. Thanks! Henrik Sjöström ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Tracula with multi-shell data?
Hi! I have some questions regarding Tracula and multi-shell DWI. -Is it possible to activate the multi-shell model within bedpostx when running it through tracula? -does anyone have experience on running multi-shell data through Tracula (2 or 3 crossing fibers)? We are planning an experiment and discussing protocols consisting of around 32 directions with b=1000 and 64 directions at b=2500 so I'm looking for opinions on this with regard to Tracula processing. Thanks! Henrik Sjöström ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Tracula with multi-shell data
Dear Anastasia et al.
I have data DTI that has multiple b-values. I worked around this by
skipping '-tensor', and sym linking 'mean_fsumsamples.nii.gz' to
'dtifit_FA.nii.gz'. However, at the end of 'trac-path', there is an
error thrown. Specifically when 'dmri_pathstats' is called, because it
is looking for dtifit_{L1, L2, L3, V1, ...}. Do you have a workaround
for this? Should I just run dtifit on the data?
Also, merged_avg33_mni_bbr.nii.gz wasn't created, but I was able to
create it (I copied the code from around line 400 of 'trac-paths'). When
I view it with freeview, though, there is a light blue/greenish
background. I assume those voxels are supposed to be 0's, but for some
reason aren't here?
Thanks,
Chris
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