Hi,
I have noticed that recently recon-all is taking a lot longer than usual
to finish. It used to take around 30 to 48 hours, but the last couple that
I have done are taking a whole week. It seems to get stuck in a repetitive
step and it numbers each iteration like this:
not handling expanded ventricles...
using previously computed transform transforms/talairach.lta
renormalizing sequences with structure alignment, equivalent to:
-renormalize
-regularize_mean 0.500
-regularize 0.500
using MR volume brainmask.mgz to mask input volume...
reading 1 input volumes...
logging results to talairach.log
reading input volume 'norm.mgz'...
reading GCA '/usr/local/freesurfer/stable4/average/RB_all_2008-03-26.gca'...
freeing gibbs priors...done.
average std[0] = 5.0
label assignment complete, 0 changed (0.00%)
det(m_affine) = 1.30 (predicted orig area = 6.2)
label assignment complete, 0 changed (0.00%)
**************** pass 1 of 1 ************************
setting smoothness coefficient to 0.04
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.759, neg=0, invalid=766
0001: dt=252.406048, rms=0.710 (6.426%), neg=0, invalid=766
0002: dt=157.425287, rms=0.695 (2.149%), neg=0, invalid=766
0003: dt=199.529412, rms=0.687 (1.109%), neg=0, invalid=766
0004: dt=115.649123, rms=0.684 (0.433%), neg=0, invalid=766
0005: dt=517.888000, rms=0.677 (1.076%), neg=0, invalid=766
0006: dt=74.457516, rms=0.675 (0.226%), neg=0, invalid=766
0007: dt=74.457516, rms=0.675 (0.073%), neg=0, invalid=766
0008: dt=74.457516, rms=0.674 (0.143%), neg=0, invalid=766
0009: dt=74.457516, rms=0.672 (0.227%), neg=0, invalid=766
0010: dt=74.457516, rms=0.670 (0.292%), neg=0, invalid=766
0011: dt=74.457516, rms=0.668 (0.289%), neg=0, invalid=766
0012: dt=74.457516, rms=0.667 (0.258%), neg=0, invalid=766
0013: dt=74.457516, rms=0.665 (0.229%), neg=0, invalid=766
0014: dt=74.457516, rms=0.664 (0.195%), neg=0, invalid=766
0015: dt=74.457516, rms=0.663 (0.191%), neg=0, invalid=766
0016: dt=74.457516, rms=0.661 (0.213%), neg=0, invalid=766
0017: dt=74.457516, rms=0.660 (0.192%), neg=0, invalid=766
0018: dt=74.457516, rms=0.659 (0.154%), neg=0, invalid=766
0019: dt=74.457516, rms=0.658 (0.132%), neg=0, invalid=766
0020: dt=74.457516, rms=0.657 (0.119%), neg=0, invalid=766
0021: dt=74.457516, rms=0.656 (0.140%), neg=0, invalid=766
0022: dt=74.457516, rms=0.655 (0.162%), neg=0, invalid=766
0023: dt=74.457516, rms=0.654 (0.162%), neg=0, invalid=766
0024: dt=74.457516, rms=0.653 (0.138%), neg=0, invalid=766
0025: dt=74.457516, rms=0.652 (0.114%), neg=0, invalid=766
0026: dt=74.457516, rms=0.652 (0.117%), neg=0, invalid=766
0027: dt=74.457516, rms=0.651 (0.130%), neg=0, invalid=766
0028: dt=74.457516, rms=0.650 (0.138%), neg=0, invalid=766
0029: dt=74.457516, rms=0.649 (0.124%), neg=0, invalid=766
0030: dt=74.457516, rms=0.649 (0.104%), neg=0, invalid=766
0031: dt=32.368000, rms=0.649 (-0.001%), neg=0, invalid=766
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.649, neg=0, invalid=766
0032: dt=129.472000, rms=0.647 (0.306%), neg=0, invalid=766
0033: dt=517.888000, rms=0.645 (0.194%), neg=0, invalid=766
0034: dt=517.888000, rms=0.645 (0.016%), neg=0, invalid=766
0035: dt=517.888000, rms=0.645 (-0.929%), neg=0, invalid=766
setting smoothness coefficient to 0.15
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.651, neg=0, invalid=766
0036: dt=51.963303, rms=0.646 (0.707%), neg=0, invalid=766
0037: dt=216.338028, rms=0.634 (1.907%), neg=0, invalid=766
0038: dt=39.422680, rms=0.630 (0.681%), neg=0, invalid=766
0039: dt=145.152000, rms=0.627 (0.498%), neg=0, invalid=766
0040: dt=73.437288, rms=0.622 (0.677%), neg=0, invalid=766
0041: dt=75.051233, rms=0.619 (0.604%), neg=0, invalid=766
0042: dt=23.040000, rms=0.618 (0.092%), neg=0, invalid=766
0043: dt=23.040000, rms=0.618 (0.058%), neg=0, invalid=766
0044: dt=23.040000, rms=0.617 (0.112%), neg=0, invalid=766
It continues to do that for days. I have run it in 2 different computers
and it makes no difference. Any ideas why this is now taking so long and
how to make a bit faster?
Thanks!
Rodrigo
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