External Email - Use Caution It’s just huge data collected from general population. Some data can have motion artifact, but I couldn’t find any special points in the protocol.
http://protocols.humanconnectome.org/HCP/3T/imaging-protocols.html <http://protocols.humanconnectome.org/HCP/3T/imaging-protocols.html> J. > On Nov 4, 2018, at 4:21 AM, Yendiki, Anastasia <ayend...@mgh.harvard.edu> > wrote: > > Hi June - Not in principle, any number of directions > 30 should be > compatible. Is there anything else that's different about this data, e.g., > SNR, motion, population with more morphological variability, etc.? > > a.y > From: freesurfer-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > <freesurfer-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of June Kang > <cn...@korea.ac.kr <mailto:cn...@korea.ac.kr>> > Sent: Saturday, November 3, 2018 12:24:54 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Tracula Question-How the threshold in final merged > tracts are defined? > > External Email - Use Caution > Thanks, Professor Anastasia, > > I am testing HCP data with 96 directions. > There are really frequent failure for right cingulum-angular bundle and right > uncinate fasciculus (more than 25%), which not happened with my own > 64-direction data with Siemens Trio. > > Is there any known issue or recommended modification of the pipeline for HCP > data or data with more directions? > > Bests, > J. > > >> On Nov 2, 2018, at 10:44 AM, Yendiki, Anastasia <ayend...@mgh.harvard.edu >> <mailto:ayend...@mgh.harvard.edu>> wrote: >> >> They are not random, they are 20% of the maximum value. If you want to >> generate stats at a different threshold, you can find the dmri_pathstats >> command line in trac-all.log and add the --pthr option (the default 20% >> would be --pthr .2). >> >> On Nov 1, 2018 9:01 PM, June Kang <cn...@korea.ac.kr >> <mailto:cn...@korea.ac.kr>> wrote: >> External Email - Use Caution >> >> In the visualization step of Tracula processing, freeview -tv >> merged_avg33_mni_bbr shows some tracts with very high threshold (i.e. 171), >> which make them look like the reconstruction-failed ones. >> The tracts failed to reconstruction usually show threshold of 300 (not >> changeable) with tiny rounded cylinder shape. >> In successfully reconstructed tracts with very high threshold, it looks ok, >> when I adjust threshold to the similar value from contralateral one. >> >> Is there any reason for this extremely high threshold? or it’s just randomly >> set values? >> >> Bests, >> J. >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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