<div dir="ltr"><font face="arial, helvetica, sans-serif">Hi Basile (and all),</font><div><font face="arial, helvetica, sans-serif"><br></font></div><div><font face="arial, helvetica, sans-serif">The difference between what was presented in the <a href="http://www.sciencedirect.com/science/article/pii/S1053811912005824">journal article</a> and the current ACT implementation is minuscule, and should only affect tracking results in voxels with more than two tissue types (which are rare).</font></div>
<div><font face="arial, helvetica, sans-serif"><br></font></div><div><font face="arial, helvetica, sans-serif">In terms of the image format, the difference is the inclusion of a fifth tissue type (hence "<a href="https://github.com/jdtournier/mrtrix3/wiki/Anatomically-Constrained-Tractography-(ACT)">5TT</a>"): 'pathological', which is the fifth of the five image volumes in the ACT image. This allows users to manually delineate regions of the brain where the nature of the underlying biology is unknown; streamlines in such regions are allowed to propagate or terminate freely, i.e. without the application of any priors from the anatomical image.</font></div>
<div><font face="arial, helvetica, sans-serif"><br></font></div><div><font face="arial, helvetica, sans-serif">I definitely agree that tissue segmentations that provide partial volume images rather than binary masks should give better tracking results. If you think of the GM-WM interface as a surface, by converting your tissue estimations into binary masks you are immediately introducing jagged edges into your reconstruction of that surface; whereas with good partial volume estimates, the sub-voxel surface along which the interpolated GM and WM fractions are equal will approximately follow the actual underlying surface.</font></div>
<div><font face="arial, helvetica, sans-serif">However this is not the only issue that I have with using FreeSurfer tissue segmentations for ACT: FreeSurfer's strength is delineation of the cortical ribbon, but it fails to segment many mid-brain structures, so the tracking does not behave as expected in those areas. If anything, this script was provided to demonstrate how tissue segmentations from any alternative software package can be manipulated into a format appropriate for ACT.</font></div>
<div><font face="arial, helvetica, sans-serif"><br></font></div><div><font face="arial, helvetica, sans-serif">The console message "<i style="font-size:13px">resampling ACT 5TT image to fixel image space"</i><span style="font-size:13px"> is appearing due to the use of dynamic seeding. This seeding method constructs the same model for comparing FOD amplitudes to streamlines densities as is used in the <a href="http://www.sciencedirect.com/science/article/pii/S1053811912011615">SIFT method</a>, and therefore requires the same definition of the processing mask in diffusion image space as is used in that method; the dynamic seeding itself is however unpublished. The precise calculation of this mask also differs slightly from that described in the ACT paper, but this response is long enough as it is...</span></font></div>
<div><span style="font-size:13px"><font face="arial, helvetica, sans-serif"><br></font></span></div><div><span style="font-size:13px"><font face="arial, helvetica, sans-serif">Regardless of whether or not you are using dynamic seeding, <u>the tracking itself <i>always</i> uses the ACT 5TT image at its provided resolution</u>. This is a big benefit of performing tracking in 'real space' as is done in MRtrix: there's no need to explicitly re-sample one image to match another and hence degrade the image resolution. From a streamline's position in real space, a single transformation and interpolation step is performed to access the diffusion image information, and (independently) another transformation and interpolation step is performed to access the tissue information. You should therefore provide the tissue segmentation image at the resolution at which it is generated.</font></span></div>
<div><font face="arial, helvetica, sans-serif"><br></font></div><div><font face="arial, helvetica, sans-serif">Best regards</font></div><div><font face="arial, helvetica, sans-serif">Rob</font></div><div class="gmail_extra">
<div><div dir="ltr"><br>--<br><br><span style="color:rgb(255,102,0)"><b>Robert Smith, Ph.D</b><br>Research Officer, Imaging Division</span><br><br>The Florey Institute of Neuroscience and Mental Health<br>Melbourne Brain Centre - Austin Campus<br>
245 Burgundy Street<br>Heidelberg Vic 3084<br>Ph: +61 3 9035 7128<br>Fax: +61 3 9035 7301<br><a href="http://www.florey.edu.au/" target="_blank">www.florey.edu.au</a><br></div></div>
<br><br><div class="gmail_quote">On Sat, Jun 21, 2014 at 12:57 AM, basile pinsard <span dir="ltr"><<a href="mailto:basile.pinsard@gmail.com" target="_blank">basile.pinsard@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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could you provide me some details about ACT in practice?<br>
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is the current version method different from what is described in the article?<br>
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Partial volume (pv) seems to give better results than converted freesurfer aparc binary maps but tckgen says:<i> resampling ACT 5TT image to fixel image space</i><br>
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<div>is that only to create the seeding mask used for dynamic seeding? in this case is that just downsampling white matter pv to the scan resolution and thresholding at .5? or to the tracking step resolution? or else?<br>
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<div>Is this resampling also performed for the partial volume values or does it interpolates dynamically from native provided 5TT?<br>
What is the best 5TT image to provide the software, is the highest resolution achievable useless?<br>
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<div>Many thanks.<br>
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<div>Cheers<span class="HOEnZb"><font color="#888888"><br>
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<div><font size="1">Basile Pinsard<br>
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<i><font size="1">PhD candidate<br>
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<font size="1">Laboratoire d'Imagerie Biomédicale, UMR S 1146 / UMR 7371, Sorbonne Universités, UPMC, INSERM, CNRS<br>
Unité de Neuroimagerie Fonctionnelle, CRIUGM, Université de Montréal</font><br>
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