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

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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