[MINC-development] -O3 breaks N3
Vladimir S. FONOV
vladimir.fonov at gmail.com
Thu Apr 19 10:59:05 EDT 2012
Hello,
I managed to track problem further. First, it turns out that on new
build volume_stats -nocache produced very different results then
default (and consistent with old build). So, I disabled caching.
On top of that, I discovered that the output of sharpen_hist changed
significantly.
If i give the following command line:
sharpen_hist -blur -fwhm .2 -noise 0.01 -range 762.440430 1646.982788
hist.txt hist.sharp.txt
the output is very different for two versions (and none of them makes
any sense whatsoever).
See attached file hist.txt, hist_old.sharp.txt and hist_new.shart.txt
the graph showing the histogram is here:
http://www.bic.mni.mcgill.ca/~vfonov/temp/histograms.png
On Wed, Apr 18, 2012 at 11:58 PM, Claude LEPAGE
<claude at bic.mni.mcgill.ca> wrote:
> Hi,
>
> I think the damping of 1.0e-7 might be a little bit too
> aggressive and not enough damping can cause the matrix
> system to be ill-conditioned. While it works in most cases,
> a value of 1.0e-6 will give similar results and will be
> more robust numerically. Can you try that?
>
> Claude
>
>> Hello Everybody,
>>
>> Turns out that N3 is broken with -O2. Actually , compiling
>> http://packages.bic.mni.mcgill.ca/tgz/N3-1.12.0.tar.gz
>> using standard ./configure & make
>>
>> produces a code which seem to work, but essentially corrects nothing at
>> least when applied to icmb 00100 t1w scan :
>> (
>> /data/ipl/user01/rotor/icbm_recovery/shell-pipe-analy-circa2006/native/mni_icbm_00100.001.t1.mnc.gz
>> on the bic system)
>>
>> it produces an imp file :
>>
>> MNI Field File
>> %Wed Apr 18 18:40:53 2012>>> /opt/minc2/bin/nu_estimate_np_and_em
>> -parzen -log -sharpen 0.1 0.01 -iterations 100 -stop 0.0001 -shrink 4
>> -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute
>> -clobber -nokeeptmp -tmpdir /tmp/nu_correct_7795/
>> mni_icbm_00100.001.t1.mnc auto_mni_icbm_00100.001.t1.nuc.imp
>> Version = 0.9.0;
>> Field_Type = B_Spline;
>> Distance = 200;
>> Domain =
>> -81.519097598907 89.3619937534825
>> -95.84404 164.15596
>> -155.813426545559 107.579156148442;
>> Coefficients =
>> 6.93367797718816e-310
>> 6.93367797718816e-310
>> 0
>> 0
>> 0
>> ...(all zeroes)
>> 0;
>>
>> When compiled on ubuntu 11.04 , gcc version 4.5.2
>>
>> Interestingly, the same tool compiled on Debian 5, gcc version 4.3.4
>> works as expected.
>>
>>
>>
>>
>> On 12-04-15 07:41 AM, Andrew Janke wrote:
>> > Absolutely...
>> >
>> > Claude, remember also the bug we fixed in EBTKS's spline
>> > implementation a long time back that was causing crashed on some files
>> > with certain magic dimensions. I can't think of how this might break
>> > anything (we added an episilon IIRC) but it was a change we had to
>> > make.
>> >
>> > I for one am keen to keep N3 as it is and I don't see it being a
>> > problem to force -02 behaviour during the compile. I have used N4 but
>> > often revert to N3, probably because it's a beast I know.
>>
>>
>> --
>> Best regards,
>>
>> Vladimir S. FONOV ~ vladimir <dot> fonov <at> gmail <dot> com
>> _______________________________________________
>> MINC-development mailing list
>> MINC-development at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>>
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
--
Best regards,
Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
-------------- next part --------------
# histogram for class 1
# domain: 762.440430 1646.982788
# entropy: 6.01581
# bin centers counts
762.440430 1.447669
766.885366 0.552331
771.330303 3.073278
775.775239 0.926722
780.220176 0.000000
784.665112 0.850277
789.110049 3.817778
793.554985 6.906856
797.999921 6.762096
802.444858 7.913423
806.889794 6.777823
811.334731 5.608207
815.779667 6.814382
820.224604 6.449176
824.669540 6.559679
829.114477 6.088694
833.559413 4.173958
838.004350 3.679496
842.449286 3.735304
846.894223 2.473919
851.339159 4.580214
855.784096 5.400192
860.229032 7.675963
864.673969 6.646347
869.118905 10.421378
873.563842 6.474981
878.008778 4.486738
882.453714 1.905386
886.898651 0.825353
891.343587 2.470996
895.788524 7.367927
900.233460 6.913462
904.678397 7.428470
909.123333 9.801539
913.568270 5.002294
918.013206 1.987693
922.458143 0.000000
926.903079 0.053249
931.348016 1.461231
935.792952 2.753523
940.237889 7.306238
944.682825 7.260273
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953.572698 5.903782
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993.577126 5.112484
998.022063 6.355876
1002.466999 8.477482
1006.911936 11.317079
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1646.982788 24.999533
-------------- next part --------------
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0.819095 1486.965075
0.824121 1491.410011
0.829146 1495.854948
0.834171 1500.299884
0.839196 1504.744821
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0.849246 1513.634694
0.854271 1518.079630
0.859296 1522.524567
0.864322 1526.969503
0.869347 1531.414440
0.874372 1535.859376
0.879397 1540.304313
0.884422 1544.749249
0.889447 1549.194186
0.894472 1553.639122
0.899497 1558.084059
0.904523 1562.528995
0.909548 1566.973931
0.914573 1571.418868
0.919598 1575.863804
0.924623 1580.308741
0.929648 1584.753677
0.934673 1589.198614
0.939698 1593.643550
0.944724 1598.088487
0.949749 1602.533423
0.954774 1606.978360
0.959799 1611.423296
0.964824 1615.868233
0.969849 1620.313169
0.974874 1624.758106
0.979899 1629.203042
0.984925 1633.647979
0.989950 1638.092915
0.994975 1642.537852
1.000000 1646.982788
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