Hi Shantanu - It's stuck trying to initialize one of the tracts. You can check which tract it is, and then check the data to see if there's something wrong that would affect that particular tract (for example, if part of the brain that this tract goes through is cut off in the mask).
a.y On Fri, 1 Aug 2014, Shantanu Ghosh wrote: > Hi Freesurfer experts, > > I ran the command <trac-all -prep -c dmrirc.txt> > > on a bunch of subjects and all of them finished in ~90 minutes except one. > This subject keeps on going into a seemingly endless loop. It has been > running for almost 12 hours now. A section of the console output is > reproduced below. > > What is the issue here, and how can this be solved? > I am using the dev version on a Linux box. > > Thanks in advance for all help. > Shantanu > > ------ > SAMPLE CONSOLE OUTPUT > ------ > INFO: Distances between consecutive points in test subject's space are 11 > 11 10 10 10 > WARN: Could not find satisfactory control point fit - try 1831 > Finding center streamline > INFO: Step is 5 voxels > WARN: Turning off deviation check for center streamline > INFO: Step is 5 voxels > WARN: Turning off FA check for center streamline > INFO: Step is 5 voxels > INFO: Length of center streamline is 91 voxels > Selecting 6 points on center streamline > INFO: Minimum allowable distance between dominant points is 9 > INFO: Minimum allowable curvature at a dominant point is 0.0283381 > INFO: Points where local peeks in curvature occur are > 106 105 67 (curv = 0.0284049) > 112 108 77 (curv = 0.0450985) > 115 108 98 (curv = 0.0526145) > 113 104 116 (curv = 0.0460477) > 107 103 128 (curv = 0.0759711) > INFO: Intermediate dominant points are > 103 98 50 > 112 108 77 > 114 108 89 > 115 108 98 > 107 103 128 > 105 106 145 > INFO: Final dominant points are > 103 98 50 > 112 108 77 > 114 108 89 > 115 108 98 > 107 103 128 > 105 106 145 > WARN: Defaulting to equidistant dominant points > WARN: Defaulting to equidistant control points > INFO: Selected control points are > 103 98 50 > 108 106 69 > 114 108 89 > 114 105 108 > 108 103 126 > 105 106 145 > INFO: Distances between consecutive points are 21 21 19 19 19 > INFO: Selected control points in test subject's space are > 80 62 23 > 81 66 31 > 84 68 40 > 84 66 48 > 82 64 56 > 81 65 64 > INFO: Distances between consecutive points in test subject's space are 9 > 10 8 8 8 > WARN: Could not find satisfactory control point fit - try 1832 > Finding center streamline > INFO: Step is 5 voxels > WARN: Turning off deviation check for center streamline > INFO: Step is 5 voxels > WARN: Turning off FA check for center streamline > INFO: Step is 5 voxels > > > > > _______________________________________________ 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.
