Hi Gang,

I'm getting a new (for me) error message at the very end of the 3dLME run. I couldn't find it mentioned with a cursory look, maybe you can help. I have the latest binaries, and I'm using R 2.15.3. I've run other 3dLMEs (with older binaries, same R version), on this machine with no problem. I'll try running one of those tonight to see if I get the same error. It takes a couple more hours to run than this one does so wanted to get your input early.

Thanks so much.
Hugo

afni -ver
Version AFNI_2011_12_21_1014
[[Precompiled binary macosx_10.7_Intel_64: Jan 8 2014]]


error message:
Error in if (bb == 0 | bb == -1) for (n in 1:dim(summary(fm)$tTable)[1]) statpar <- paste(statpar, :
missing value where TRUE/FALSE needed
Execution halted

3dLME command:

set behav_dir='/Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/GROUP'

3dLME -prefix ${behav_dir}/PPI/3DLME_Dx_Session_20140110 \
-mask ${behav_dir}/final_group_mask+tlrc \
-jobs 4 \
-model "time*diagnosis" \
-ranEff '~1' -SS_type 1 \
-dataTable \
Subj time diagnosis InputFile \
'1014 s1 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/10.results/PPI/10-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'2525 s1 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/25.results/PPI/25-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'4952 s1 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/49.results/PPI/49-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'5151 s1 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/51.results/PPI/51-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'5664 s1 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/56.results/PPI/56-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'8282 s1 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/82.results/PPI/82-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'1723 s1 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/17.results/PPI/17-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'1824 s1 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/18.results/PPI/18-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'3034 s1 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/30.results/PPI/30-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'3239 s1 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/32.results/PPI/32-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'3742 s1 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/37.results/PPI/37-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'3844 s1 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/38.results/PPI/38-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'4045 s1 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/40.results/PPI/40-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'5968 s1 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/59.results/PPI/59-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'6367 s1 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/63.results/PPI/63-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'6570 s1 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/65.results/PPI/65-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'6975 s1 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/69.results/PPI/69-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'7278 s1 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/72.results/PPI/72-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'8385 s1 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/83.results/PPI/83-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'8690 s1 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/86.results/PPI/86-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'8891 s1 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/88.results/PPI/88-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'1723 s2 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/23.results/PPI/23-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'1824 s2 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/24.results/PPI/24-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'3034 s2 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/34.results/PPI/34-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'3239 s2 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/39.results/PPI/39-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'3742 s2 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/42.results/PPI/42-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'3844 s2 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/44.results/PPI/44-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'4045 s2 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/45.results/PPI/45-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'5968 s2 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/68.results/PPI/68-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'6367 s2 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/67.results/PPI/67-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'6570 s2 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/70.results/PPI/70-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'6975 s2 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/75.results/PPI/75-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'7278 s2 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/78.results/PPI/78-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'8385 s2 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/85.results/PPI/85-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'8690 s2 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/90.results/PPI/90-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'8891 s2 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/91.results/PPI/91-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'0103 s2 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/03.results/PPI/03-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'1316 s2 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/16.results/PPI/16-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'6271 s2 AN /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/71.results/PPI/71-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'2027 s1 HC /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/20.results/PPI/20-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'2833 s1 HC /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/28.results/PPI/28-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'2936 s1 HC /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/29.results/PPI/29-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'3148 s1 HC /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/31.results/PPI/31-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'4347 s1 HC /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/43.results/PPI/43-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'5054 s1 HC /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/50.results/PPI/50-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'5360 s1 HC /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/53.results/PPI/53-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'6673 s1 HC /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/66.results/PPI/66-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'7681 s1 HC /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/76.results/PPI/76-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'8084 s1 HC /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/80.results/PPI/80-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'8794 s1 HC /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/87.results/PPI/87-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'8995 s1 HC /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/89.results/PPI/89-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'9296 s1 HC /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/92.results/PPI/92-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'9398 s1 HC /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/93.results/PPI/93-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'0208 s1 HC /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/02.results/PPI/02-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'0404 s1 HC /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/04.results/PPI/04-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'1919 s1 HC /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/19.results/PPI/19-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'2635 s1 HC /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/26.results/PPI/26-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'7474 s1 HC /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/74.results/PPI/74-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'9797 s1 HC /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/97.results/PPI/97-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'2027 s2 HC /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/27.results/PPI/27-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'2833 s2 HC /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/33.results/PPI/33-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'2936 s2 HC /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/36.results/PPI/36-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'3148 s2 HC /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/48.results/PPI/48-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'4347 s2 HC /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/47.results/PPI/47-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'5054 s2 HC /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/54.results/PPI/54-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'5360 s2 HC /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/60.results/PPI/60-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'6673 s2 HC /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/73.results/PPI/73-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'7681 s2 HC /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/81.results/PPI/81-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'8084 s2 HC /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/84.results/PPI/84-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'8794 s2 HC /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/94.results/PPI/94-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'8995 s2 HC /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/95.results/PPI/95-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'9296 s2 HC /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/96.results/PPI/96-PPI-deconvolve+tlrc[PPI#0_Coef]' \
'9398 s2 HC /Volumes/BuckleyProjects/KlarmanAN/Imaging/ANALYSIS_Hugo/98.results/PPI/98-PPI-deconvolve+tlrc[PPI#0_Coef]'

Output:
Loading required package: nlme
Loading required package: contrast
Loading required package: rms
Loading required package: Hmisc
Loading required package: survival
Loading required package: splines
Hmisc library by Frank E Harrell Jr

Type library(help='Hmisc'), ?Overview, or ?Hmisc.Overview')
to see overall documentation.

NOTE:Hmisc no longer redefines [.factor to drop unused levels when
subsetting. To get the old behavior of Hmisc type dropUnusedLevels().


Attaching package: ‘Hmisc’

The following object(s) are masked from ‘package:survival’:

untangle.specials

The following object(s) are masked from ‘package:base’:

format.pval, round.POSIXt, trunc.POSIXt, units


Attaching package: ‘rms’

The following object(s) are masked from ‘package:survival’:

Surv


++++++++++++++++++++++++++++++++++++++++++++++++++++
***** Summary information of data structure *****
44 subjects : 0103 0208 0404 1014 1316 1723 1824 1919 2027 2525 2635 2833 2936 3034 3148 3239 3742 3844 4045 4347 4952 5054 5151 5360 5664 5968 6271 6367 6570 6673 6975 7278 7474 7681 8084 8282 8385 8690 8794 8891 8995 9296 9398 9797
73 response values
2 levels for factor time : s1 s2
2 levels for factor diagnosis : AN HC
0 post hoc tests

Tabulation of subjects against all categorical variables
~~~~~~~~~~~~~~
Subj vs time:

s1 s2
0103 0 1
0208 1 0
0404 1 0
1014 1 0
1316 0 1
1723 1 1
1824 1 1
1919 1 0
2027 1 1
2525 1 0
2635 1 0
2833 1 1
2936 1 1
3034 1 1
3148 1 1
3239 1 1
3742 1 1
3844 1 1
4045 1 1
4347 1 1
4952 1 0
5054 1 1
5151 1 0
5360 1 1
5664 1 0
5968 1 1
6271 0 1
6367 1 1
6570 1 1
6673 1 1
6975 1 1
7278 1 1
7474 1 0
7681 1 1
8084 1 1
8282 1 0
8385 1 1
8690 1 1
8794 1 1
8891 1 1
8995 1 1
9296 1 1
9398 1 1
9797 1 0

~~~~~~~~~~~~~~
Subj vs diagnosis:

AN HC
0103 1 0
0208 0 1
0404 0 1
1014 1 0
1316 1 0
1723 2 0
1824 2 0
1919 0 1
2027 0 2
2525 1 0
2635 0 1
2833 0 2
2936 0 2
3034 2 0
3148 0 2
3239 2 0
3742 2 0
3844 2 0
4045 2 0
4347 0 2
4952 1 0
5054 0 2
5151 1 0
5360 0 2
5664 1 0
5968 2 0
6271 1 0
6367 2 0
6570 2 0
6673 0 2
6975 2 0
7278 2 0
7474 0 1
7681 0 2
8084 0 2
8282 1 0
8385 2 0
8690 2 0
8794 0 2
8891 2 0
8995 0 2
9296 0 2
9398 0 2
9797 0 1
***** End of data structure information *****
++++++++++++++++++++++++++++++++++++++++++++++++++++

Reading input files now...

[1] "Great, test run passed at voxel (18, 32, 25)!"
[1] "Start to compute 50 slices along Z axis. You can monitor the progress"
[1] "and estimate the total run time as shown below."
[1] "01/10/14 17:11:37.380"
Z slice 1 done: 01/10/14 17:11:38.816
Z slice 2 done: 01/10/14 17:11:38.855
Z slice 3 done: 01/10/14 17:11:38.896
Z slice 4 done: 01/10/14 17:11:38.937
Z slice 5 done: 01/10/14 17:11:38.998
Z slice 6 done: 01/10/14 17:11:39.820
Z slice 7 done: 01/10/14 17:11:46.582
Z slice 8 done: 01/10/14 17:11:53.577
Z slice 9 done: 01/10/14 17:12:01.342
Z slice 10 done: 01/10/14 17:12:10.114
Z slice 11 done: 01/10/14 17:12:20.612
Z slice 12 done: 01/10/14 17:12:32.041
Z slice 13 done: 01/10/14 17:12:45.009
Z slice 14 done: 01/10/14 17:12:59.484
Z slice 15 done: 01/10/14 17:13:16.913
Z slice 16 done: 01/10/14 17:13:35.758
Z slice 17 done: 01/10/14 17:13:56.404
Z slice 18 done: 01/10/14 17:14:19.670
Z slice 19 done: 01/10/14 17:14:44.462
Z slice 20 done: 01/10/14 17:15:10.768
Z slice 21 done: 01/10/14 17:15:38.400
Z slice 22 done: 01/10/14 17:16:07.349
Z slice 23 done: 01/10/14 17:16:36.809
Z slice 24 done: 01/10/14 17:17:05.253
Z slice 25 done: 01/10/14 17:17:32.988
Z slice 26 done: 01/10/14 17:18:01.047
Z slice 27 done: 01/10/14 17:18:28.252
Z slice 28 done: 01/10/14 17:18:55.955
Z slice 29 done: 01/10/14 17:19:24.063
Z slice 30 done: 01/10/14 17:19:52.201
Z slice 31 done: 01/10/14 17:20:20.013
Z slice 32 done: 01/10/14 17:20:47.738
Z slice 33 done: 01/10/14 17:21:15.736
Z slice 34 done: 01/10/14 17:21:42.501
Z slice 35 done: 01/10/14 17:22:08.580
Z slice 36 done: 01/10/14 17:22:34.378
Z slice 37 done: 01/10/14 17:22:58.804
Z slice 38 done: 01/10/14 17:23:22.641
Z slice 39 done: 01/10/14 17:23:44.779
Z slice 40 done: 01/10/14 17:24:04.022
Z slice 41 done: 01/10/14 17:24:21.341
Z slice 42 done: 01/10/14 17:24:36.707
Z slice 43 done: 01/10/14 17:24:49.601
Z slice 44 done: 01/10/14 17:24:59.333
Z slice 45 done: 01/10/14 17:25:06.163
Z slice 46 done: 01/10/14 17:25:09.479
Z slice 47 done: 01/10/14 17:25:09.519
Z slice 48 done: 01/10/14 17:25:09.555
Z slice 49 done: 01/10/14 17:25:09.593
Z slice 50 done: 01/10/14 17:25:09.662
Error in if (bb == 0 | bb == -1) for (n in 1:dim(summary(fm)$tTable)[1]) statpar <- paste(statpar, :
missing value where TRUE/FALSE needed
Execution halted