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Dear AFNI users-
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
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Sincerely, AFNI HQ
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
https://discuss.afni.nimh.nih.gov
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely, AFNI HQ
| March 28, 2010 09:13PM | |
Hi all
I'm experiencing an error message with GroupAna that is completely new to me. I've done all the troubleshooting I can think of ---very similar scripts have worked as recently as last month, with the only changes being the number of subjects and the input pathway for the glm. It's a simple two way anova with first factor controllablity (control, no control), second factor stimulus (snake, fish) and third factor subject (random). I have 2 first order contrasts and 4 third order contrasts. Everything matches up.
1) Here are the errors:
Done with 3rd order contrast information.
??? Reference to non-existent field 'idx3'.
Error in ==> ContrVec at 328
switch Contr.ord3.cnt(i).idx3
Error in ==> PreProc at 352
[err, Contr] = ContrVec(3, n, NF, group, dmat, Contr, FL, num_col);
Error in ==> GroupAna at 1631
[err, Qd, s, termname, nterms, sindices, dfbothSS, modw, modwo, tnames, dfterm, dfe, Contr] =
PreProc(ntot, NF, group, varnames, FL, Contr, cov, unbalanced);
2) I have also pasted the full screen output of the entire running process of the ANOVA -- complete with the above errors that appear at the end of the output -- at the bottom of this email.
Many thanks for any help / ideas for further troubleshooting.
Deborah
---FULL SCREEN OUTPUT WITH ERRORS---
[kerr@caloro processed]$ nice -n11 matlab -nodesktop
Warning: No display specified. You will not be able to display graphics on the screen.
Warning: No window system found. Java option 'MWT' ignored
< M A T L A B (R) >
Copyright 1984-2009 The MathWorks, Inc.
Version 7.8.0.347 (R2009a) 64-bit (glnxa64)
February 12, 2009
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
>> addpath('/study/anxdep/Data/AnxDep_fMRI/DesWork/afni_matlab/matlab/')
>> GroupAna
Welcome to GroupAna, AFNI Group Analysis Package!
-----------------------------------------------------------
Version 1.0.1, Nov. 23, 2005
Author: Gang Chen
SSCC/NIMH/ National Institutes of Health, Bethesda MD 20892
-----------------------------------------------------------
Please read the following carefully about group analysis setup:
1. If the resolution of your EPI data is near n millimeters, during Talairach conversion use
"the command adwarp -dxyz n" to greatly reduce runtime without sacrificing accuracy.
2. We strongly suggest that factor names be labeled with short (2 or 3 capital letters) names
so that subbrik labels can be shown on AFNI viewer.
3. With nesting, arrange your design in such a way that the last factor is nested within the 1st factor.
4. Each input file should include only one subbrik. We suggest files be
named by reflecting the hierarchy of the experiment design.
5. Currently all of the following terms are modeled: main effects and applicable interactions in various orders, .
Groups analysis for volume or surface data (0 - volume; 1 - surface)? 0
How many factors? 3
Availabe design types:
Type 1: Factorial (crossed) design AXBXC - all factors are fixed.
Type 2: Factorial (crossed) design AXBXC - factors A and B are fixed while C is random. If C is subject, it is
usually called 2-way design with A and B varying within subject. Notice: It is inappropriate to
run any constrast tests including mean estimates and differences for factor C with this design type.
Type 3: Mixed design BXC(A) - A and B are fixed while C (usually subject) is random and nested within A.
Type 4: Mixed design BXC(A) - Fixed factor C is nested within fixed factor A while B (usually subject) is random.
Choose design type (1, 2, 3, 4, 5): 2
Is the design balanced? (1 - Yes; 0 - No) 1
Label for No. 1 factor: Cont
How many levels does factor A (Cont) have? 2
Label for No. 1 level of factor A (Cont) is: c
Label for No. 2 level of factor A (Cont) is: nc
Label for No. 2 factor: Stim
How many levels does factor B (Stim) have? 2
Label for No. 1 level of factor B (Stim) is: S
Label for No. 2 level of factor B (Stim) is: F
Label for No. 3 factor: Sbj
How many levels does factor C (Sbj) have? 11
Label for No. 1 level of factor C (Sbj) is: MS15
Label for No. 2 level of factor C (Sbj) is: MS16
Label for No. 3 level of factor C (Sbj) is: MS18
Label for No. 4 level of factor C (Sbj) is: MS19
Label for No. 5 level of factor C (Sbj) is: MS28
Label for No. 6 level of factor C (Sbj) is: MS41
Label for No. 7 level of factor C (Sbj) is: MS47
Label for No. 8 level of factor C (Sbj) is: MS64
Label for No. 9 level of factor C (Sbj) is: MS70
Label for No. 10 level of factor C (Sbj) is: MS83
Label for No. 11 level of factor C (Sbj) is: MS88
Enter the sample size (number of observations) per combination: 1
All input files are supposed to contain only one subbrik.
There should be totally 44 input files.
Correct? (1 - Yes; 0 - No) 1
Please provide input files.
(1) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 1 (MS15)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject15/er/MS15_GLM_SPM/ppi/con_0005_TT452+tlrc.BRIK
(2) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 2 (MS16)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject16/er/MS16_GLM_SPM/ppi/con_0005_TT452+tlrc.BRIK
(3) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 3 (MS18)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject18/er/MS18_GLM_SPM/ppi/con_0005_TT452+tlrc.BRIK
(4) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 4 (MS19)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject19/er/MS19_GLM_SPM/ppi/con_0005_TT452+tlrc.BRIK
(5) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 5 (MS28)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject28/er/MS28_GLM_SPM/ppi/con_0005_TT452+tlrc.BRIK
(6) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 6 (MS41)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject41/er/MS41_GLM_SPM/ppi/con_0005_TT452+tlrc.BRIK
(7) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 7 (MS47)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject47/er/MS47_GLM_SPM/ppi/con_0005_TT452+tlrc.BRIK
(8) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 8 (MS64)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject64/er/MS64_GLM_SPM/ppi/con_0005_TT452+tlrc.BRIK
(9) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 9 (MS70)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject70/er/MS70_GLM_SPM/ppi/con_0005_TT452+tlrc.BRIK
(10) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 10 (MS83)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject83/er/MS83_GLM_SPM/ppi/con_0005_TT452+tlrc.BRIK
(11) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 11 (MS88)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject88/er/MS88_GLM_SPM/ppi/con_0005_TT452+tlrc.BRIK
(12) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 1 (MS15)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject15/er/MS15_GLM_SPM/ppi/con_0003_TT452+tlrc.BRIK
(13) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 2 (MS16)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject16/er/MS16_GLM_SPM/ppi/con_0003_TT452+tlrc.BRIK
(14) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 3 (MS18)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject18/er/MS18_GLM_SPM/ppi/con_0003_TT452+tlrc.BRIK
(15) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 4 (MS19)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject19/er/MS19_GLM_SPM/ppi/con_0003_TT452+tlrc.BRIK
(16) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 5 (MS28)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject28/er/MS28_GLM_SPM/ppi/con_0003_TT452+tlrc.BRIK
(17) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 6 (MS41)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject41/er/MS41_GLM_SPM/ppi/con_0003_TT452+tlrc.BRIK
(18) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 7 (MS47)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject47/er/MS47_GLM_SPM/ppi/con_0003_TT452+tlrc.BRIK
(19) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 8 (MS64)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject64/er/MS64_GLM_SPM/ppi/con_0003_TT452+tlrc.BRIK
(20) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 9 (MS70)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject70/er/MS70_GLM_SPM/ppi/con_0003_TT452+tlrc.BRIK
(21) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 10 (MS83)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject83/er/MS83_GLM_SPM/ppi/con_0003_TT452+tlrc.BRIK
(22) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 11 (MS88)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject88/er/MS88_GLM_SPM/ppi/con_0003_TT452+tlrc.BRIK
(23) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 1 (MS15)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject15/er/MS15_GLM_SPM/ppi/con_0006_TT452+tlrc.BRIK
(24) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 2 (MS16)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject16/er/MS16_GLM_SPM/ppi/con_0006_TT452+tlrc.BRIK
(25) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 3 (MS18)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject18/er/MS18_GLM_SPM/ppi/con_0006_TT452+tlrc.BRIK
(26) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 4 (MS19)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject19/er/MS19_GLM_SPM/ppi/con_0006_TT452+tlrc.BRIK
(27) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 5 (MS28)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject28/er/MS28_GLM_SPM/ppi/con_0006_TT452+tlrc.BRIK
(28) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 6 (MS41)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject41/er/MS41_GLM_SPM/ppi/con_0006_TT452+tlrc.BRIK
(29) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 7 (MS47)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject47/er/MS47_GLM_SPM/ppi/con_0006_TT452+tlrc.BRIK
(30) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 8 (MS64)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject64/er/MS64_GLM_SPM/ppi/con_0006_TT452+tlrc.BRIK
(31) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 9 (MS70)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject70/er/MS70_GLM_SPM/ppi/con_0006_TT452+tlrc.BRIK
(32) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 10 (MS83)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject83/er/MS83_GLM_SPM/ppi/con_0006_TT452+tlrc.BRIK
(33) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 11 (MS88)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject88/er/MS88_GLM_SPM/ppi/con_0006_TT452+tlrc.BRIK
(34) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 1 (MS15)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject15/er/MS15_GLM_SPM/ppi/con_0004_TT452+tlrc.BRIK
(35) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 2 (MS16)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject16/er/MS16_GLM_SPM/ppi/con_0004_TT452+tlrc.BRIK
(36) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 3 (MS18)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject18/er/MS18_GLM_SPM/ppi/con_0004_TT452+tlrc.BRIK
(37) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 4 (MS19)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject19/er/MS19_GLM_SPM/ppi/con_0004_TT452+tlrc.BRIK
(38) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 5 (MS28)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject28/er/MS28_GLM_SPM/ppi/con_0004_TT452+tlrc.BRIK
(39) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 6 (MS41)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject41/er/MS41_GLM_SPM/ppi/con_0004_TT452+tlrc.BRIK
(40) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 7 (MS47)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject47/er/MS47_GLM_SPM/ppi/con_0004_TT452+tlrc.BRIK
(41) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 8 (MS64)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject64/er/MS64_GLM_SPM/ppi/con_0004_TT452+tlrc.BRIK
(42) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 9 (MS70)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject70/er/MS70_GLM_SPM/ppi/con_0004_TT452+tlrc.BRIK
(43) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 10 (MS83)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject83/er/MS83_GLM_SPM/ppi/con_0004_TT452+tlrc.BRIK
(44) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 11 (MS88)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject88/er/MS88_GLM_SPM/ppi/con_0004_TT452+tlrc.BRIK
Output file name (in bucket format): /study/snkphob/DATA/MS_Data/fMRI/processed/gam_analyses/SPM_PPI_N11_phob_CxS_nodisg_anova
Any contrast test (1 - Yes, 0 - No)? 1
Now coding contrasts:
1. Each contrast should contain at least 2 terms;
2. Each term in a contrast should have 3 character(s),
No. 1 character corresponds to the level of factor A (Cont),
No. 2 character corresponds to the level of factor B (Stim),
No. 3 character corresponds to the level of factor C (Sbj),
Use 0 if a factor is collapsed.
If a factor level is smaller than 9, use its ordinal number;
If a factor level is bigger than 9, use a, b, c, ... (no capitals) for 10, 11, 12, ...
3. All weights/coeficients in a contrast have to add up to zero.
1st order contrasts have 2 factor(s) collapsed.
Notice: Contrasts for random factor are NOT feasible.
How many 1st-order contrasts? (0 if none) 2
Label for 1st order contrast No. 1 is: c-nc
How many terms are involved in this contrast? 2
Factor index for No. 1 term is (e.g., 0020): 100
Corresponding coefficient (e.g., 1 or -1): 1
Factor index for No. 2 term is (e.g., 0020): 200
Corresponding coefficient (e.g., 1 or -1): -1
Label for 1st order contrast No. 2 is: S-F
How many terms are involved in this contrast? 2
Factor index for No. 1 term is (e.g., 0020): 010
Corresponding coefficient (e.g., 1 or -1): 1
Factor index for No. 2 term is (e.g., 0020): 020
Corresponding coefficient (e.g., 1 or -1): -1
Done with 1st order contrast information.
2nd order contrasts have 1 factor(s) collapsed.
Notice: Contrasts for random factor are NOT feasible.
How many 2nd-order contrasts? (0 if none) 0
Done with 2nd order contrast information.
3rd order contrasts have 0 factor(s) collapsed.
Notice: Contrasts for random factor are NOT feasible.
How many 3rd-order contrasts? (0 if none) 4
Label for 3rd order contrast No. 1 is: PcS-PncS
How many terms are involved in this contrast? 2
Factor index for No. 1 term is (e.g., 1230): 110
Corresponding coefficient (e.g., 1 or -1): 1
Factor index for No. 2 term is (e.g., 1230): 210
Corresponding coefficient (e.g., 1 or -1): -1
Label for 3rd order contrast No. 2 is: PcF-PncF
How many terms are involved in this contrast? 2
Factor index for No. 1 term is (e.g., 1230): 120
Corresponding coefficient (e.g., 1 or -1): 1
Factor index for No. 2 term is (e.g., 1230): 220
Corresponding coefficient (e.g., 1 or -1): -1
Label for 3rd order contrast No. 3 is: PcS-PcF
How many terms are involved in this contrast? 2
Factor index for No. 1 term is (e.g., 1230): 110
Corresponding coefficient (e.g., 1 or -1): 1
Factor index for No. 2 term is (e.g., 1230): 120
Corresponding coefficient (e.g., 1 or -1): -1
Label for 3rd order contrast No. 4 is: PncS-PncF
How many terms are involved in this contrast? 2
Factor index for No. 1 term is (e.g., 1230): 210
Corresponding coefficient (e.g., 1 or -1): 1
Factor index for No. 2 term is (e.g., 1230): 220
Corresponding coefficient (e.g., 1 or -1): -1
Done with 3rd order contrast information.
??? Reference to non-existent field 'idx3'.
Error in ==> ContrVec at 328
switch Contr.ord3.cnt(i).idx3
Error in ==> PreProc at 352
[err, Contr] = ContrVec(3, n, NF, group, dmat, Contr, FL, num_col);
Error in ==> GroupAna at 1631
[err, Qd, s, termname, nterms, sindices, dfbothSS, modw, modwo, tnames, dfterm, dfe, Contr] =
PreProc(ntot, NF, group, varnames, FL, Contr, cov, unbalanced);
>>
I'm experiencing an error message with GroupAna that is completely new to me. I've done all the troubleshooting I can think of ---very similar scripts have worked as recently as last month, with the only changes being the number of subjects and the input pathway for the glm. It's a simple two way anova with first factor controllablity (control, no control), second factor stimulus (snake, fish) and third factor subject (random). I have 2 first order contrasts and 4 third order contrasts. Everything matches up.
1) Here are the errors:
Done with 3rd order contrast information.
??? Reference to non-existent field 'idx3'.
Error in ==> ContrVec at 328
switch Contr.ord3.cnt(i).idx3
Error in ==> PreProc at 352
[err, Contr] = ContrVec(3, n, NF, group, dmat, Contr, FL, num_col);
Error in ==> GroupAna at 1631
[err, Qd, s, termname, nterms, sindices, dfbothSS, modw, modwo, tnames, dfterm, dfe, Contr] =
PreProc(ntot, NF, group, varnames, FL, Contr, cov, unbalanced);
2) I have also pasted the full screen output of the entire running process of the ANOVA -- complete with the above errors that appear at the end of the output -- at the bottom of this email.
Many thanks for any help / ideas for further troubleshooting.
Deborah
---FULL SCREEN OUTPUT WITH ERRORS---
[kerr@caloro processed]$ nice -n11 matlab -nodesktop
Warning: No display specified. You will not be able to display graphics on the screen.
Warning: No window system found. Java option 'MWT' ignored
< M A T L A B (R) >
Copyright 1984-2009 The MathWorks, Inc.
Version 7.8.0.347 (R2009a) 64-bit (glnxa64)
February 12, 2009
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
>> addpath('/study/anxdep/Data/AnxDep_fMRI/DesWork/afni_matlab/matlab/')
>> GroupAna
Welcome to GroupAna, AFNI Group Analysis Package!
-----------------------------------------------------------
Version 1.0.1, Nov. 23, 2005
Author: Gang Chen
SSCC/NIMH/ National Institutes of Health, Bethesda MD 20892
-----------------------------------------------------------
Please read the following carefully about group analysis setup:
1. If the resolution of your EPI data is near n millimeters, during Talairach conversion use
"the command adwarp -dxyz n" to greatly reduce runtime without sacrificing accuracy.
2. We strongly suggest that factor names be labeled with short (2 or 3 capital letters) names
so that subbrik labels can be shown on AFNI viewer.
3. With nesting, arrange your design in such a way that the last factor is nested within the 1st factor.
4. Each input file should include only one subbrik. We suggest files be
named by reflecting the hierarchy of the experiment design.
5. Currently all of the following terms are modeled: main effects and applicable interactions in various orders, .
Groups analysis for volume or surface data (0 - volume; 1 - surface)? 0
How many factors? 3
Availabe design types:
Type 1: Factorial (crossed) design AXBXC - all factors are fixed.
Type 2: Factorial (crossed) design AXBXC - factors A and B are fixed while C is random. If C is subject, it is
usually called 2-way design with A and B varying within subject. Notice: It is inappropriate to
run any constrast tests including mean estimates and differences for factor C with this design type.
Type 3: Mixed design BXC(A) - A and B are fixed while C (usually subject) is random and nested within A.
Type 4: Mixed design BXC(A) - Fixed factor C is nested within fixed factor A while B (usually subject) is random.
Choose design type (1, 2, 3, 4, 5): 2
Is the design balanced? (1 - Yes; 0 - No) 1
Label for No. 1 factor: Cont
How many levels does factor A (Cont) have? 2
Label for No. 1 level of factor A (Cont) is: c
Label for No. 2 level of factor A (Cont) is: nc
Label for No. 2 factor: Stim
How many levels does factor B (Stim) have? 2
Label for No. 1 level of factor B (Stim) is: S
Label for No. 2 level of factor B (Stim) is: F
Label for No. 3 factor: Sbj
How many levels does factor C (Sbj) have? 11
Label for No. 1 level of factor C (Sbj) is: MS15
Label for No. 2 level of factor C (Sbj) is: MS16
Label for No. 3 level of factor C (Sbj) is: MS18
Label for No. 4 level of factor C (Sbj) is: MS19
Label for No. 5 level of factor C (Sbj) is: MS28
Label for No. 6 level of factor C (Sbj) is: MS41
Label for No. 7 level of factor C (Sbj) is: MS47
Label for No. 8 level of factor C (Sbj) is: MS64
Label for No. 9 level of factor C (Sbj) is: MS70
Label for No. 10 level of factor C (Sbj) is: MS83
Label for No. 11 level of factor C (Sbj) is: MS88
Enter the sample size (number of observations) per combination: 1
All input files are supposed to contain only one subbrik.
There should be totally 44 input files.
Correct? (1 - Yes; 0 - No) 1
Please provide input files.
(1) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 1 (MS15)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject15/er/MS15_GLM_SPM/ppi/con_0005_TT452+tlrc.BRIK
(2) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 2 (MS16)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject16/er/MS16_GLM_SPM/ppi/con_0005_TT452+tlrc.BRIK
(3) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 3 (MS18)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject18/er/MS18_GLM_SPM/ppi/con_0005_TT452+tlrc.BRIK
(4) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 4 (MS19)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject19/er/MS19_GLM_SPM/ppi/con_0005_TT452+tlrc.BRIK
(5) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 5 (MS28)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject28/er/MS28_GLM_SPM/ppi/con_0005_TT452+tlrc.BRIK
(6) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 6 (MS41)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject41/er/MS41_GLM_SPM/ppi/con_0005_TT452+tlrc.BRIK
(7) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 7 (MS47)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject47/er/MS47_GLM_SPM/ppi/con_0005_TT452+tlrc.BRIK
(8) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 8 (MS64)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject64/er/MS64_GLM_SPM/ppi/con_0005_TT452+tlrc.BRIK
(9) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 9 (MS70)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject70/er/MS70_GLM_SPM/ppi/con_0005_TT452+tlrc.BRIK
(10) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 10 (MS83)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject83/er/MS83_GLM_SPM/ppi/con_0005_TT452+tlrc.BRIK
(11) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 11 (MS88)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject88/er/MS88_GLM_SPM/ppi/con_0005_TT452+tlrc.BRIK
(12) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 1 (MS15)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject15/er/MS15_GLM_SPM/ppi/con_0003_TT452+tlrc.BRIK
(13) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 2 (MS16)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject16/er/MS16_GLM_SPM/ppi/con_0003_TT452+tlrc.BRIK
(14) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 3 (MS18)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject18/er/MS18_GLM_SPM/ppi/con_0003_TT452+tlrc.BRIK
(15) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 4 (MS19)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject19/er/MS19_GLM_SPM/ppi/con_0003_TT452+tlrc.BRIK
(16) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 5 (MS28)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject28/er/MS28_GLM_SPM/ppi/con_0003_TT452+tlrc.BRIK
(17) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 6 (MS41)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject41/er/MS41_GLM_SPM/ppi/con_0003_TT452+tlrc.BRIK
(18) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 7 (MS47)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject47/er/MS47_GLM_SPM/ppi/con_0003_TT452+tlrc.BRIK
(19) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 8 (MS64)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject64/er/MS64_GLM_SPM/ppi/con_0003_TT452+tlrc.BRIK
(20) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 9 (MS70)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject70/er/MS70_GLM_SPM/ppi/con_0003_TT452+tlrc.BRIK
(21) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 10 (MS83)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject83/er/MS83_GLM_SPM/ppi/con_0003_TT452+tlrc.BRIK
(22) factor combination:
factor A (Cont) at level 1 (c)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 11 (MS88)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject88/er/MS88_GLM_SPM/ppi/con_0003_TT452+tlrc.BRIK
(23) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 1 (MS15)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject15/er/MS15_GLM_SPM/ppi/con_0006_TT452+tlrc.BRIK
(24) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 2 (MS16)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject16/er/MS16_GLM_SPM/ppi/con_0006_TT452+tlrc.BRIK
(25) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 3 (MS18)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject18/er/MS18_GLM_SPM/ppi/con_0006_TT452+tlrc.BRIK
(26) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 4 (MS19)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject19/er/MS19_GLM_SPM/ppi/con_0006_TT452+tlrc.BRIK
(27) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 5 (MS28)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject28/er/MS28_GLM_SPM/ppi/con_0006_TT452+tlrc.BRIK
(28) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 6 (MS41)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject41/er/MS41_GLM_SPM/ppi/con_0006_TT452+tlrc.BRIK
(29) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 7 (MS47)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject47/er/MS47_GLM_SPM/ppi/con_0006_TT452+tlrc.BRIK
(30) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 8 (MS64)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject64/er/MS64_GLM_SPM/ppi/con_0006_TT452+tlrc.BRIK
(31) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 9 (MS70)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject70/er/MS70_GLM_SPM/ppi/con_0006_TT452+tlrc.BRIK
(32) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 10 (MS83)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject83/er/MS83_GLM_SPM/ppi/con_0006_TT452+tlrc.BRIK
(33) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 1 (S)
factor C (Sbj) at level 11 (MS88)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject88/er/MS88_GLM_SPM/ppi/con_0006_TT452+tlrc.BRIK
(34) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 1 (MS15)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject15/er/MS15_GLM_SPM/ppi/con_0004_TT452+tlrc.BRIK
(35) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 2 (MS16)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject16/er/MS16_GLM_SPM/ppi/con_0004_TT452+tlrc.BRIK
(36) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 3 (MS18)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject18/er/MS18_GLM_SPM/ppi/con_0004_TT452+tlrc.BRIK
(37) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 4 (MS19)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject19/er/MS19_GLM_SPM/ppi/con_0004_TT452+tlrc.BRIK
(38) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 5 (MS28)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject28/er/MS28_GLM_SPM/ppi/con_0004_TT452+tlrc.BRIK
(39) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 6 (MS41)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject41/er/MS41_GLM_SPM/ppi/con_0004_TT452+tlrc.BRIK
(40) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 7 (MS47)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject47/er/MS47_GLM_SPM/ppi/con_0004_TT452+tlrc.BRIK
(41) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 8 (MS64)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject64/er/MS64_GLM_SPM/ppi/con_0004_TT452+tlrc.BRIK
(42) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 9 (MS70)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject70/er/MS70_GLM_SPM/ppi/con_0004_TT452+tlrc.BRIK
(43) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 10 (MS83)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject83/er/MS83_GLM_SPM/ppi/con_0004_TT452+tlrc.BRIK
(44) factor combination:
factor A (Cont) at level 2 (nc)
factor B (Stim) at level 2 (F)
factor C (Sbj) at level 11 (MS88)
at repeat 1
is: /study/snkphob/DATA/MS_Data/fMRI/processed/subject88/er/MS88_GLM_SPM/ppi/con_0004_TT452+tlrc.BRIK
Output file name (in bucket format): /study/snkphob/DATA/MS_Data/fMRI/processed/gam_analyses/SPM_PPI_N11_phob_CxS_nodisg_anova
Any contrast test (1 - Yes, 0 - No)? 1
Now coding contrasts:
1. Each contrast should contain at least 2 terms;
2. Each term in a contrast should have 3 character(s),
No. 1 character corresponds to the level of factor A (Cont),
No. 2 character corresponds to the level of factor B (Stim),
No. 3 character corresponds to the level of factor C (Sbj),
Use 0 if a factor is collapsed.
If a factor level is smaller than 9, use its ordinal number;
If a factor level is bigger than 9, use a, b, c, ... (no capitals) for 10, 11, 12, ...
3. All weights/coeficients in a contrast have to add up to zero.
1st order contrasts have 2 factor(s) collapsed.
Notice: Contrasts for random factor are NOT feasible.
How many 1st-order contrasts? (0 if none) 2
Label for 1st order contrast No. 1 is: c-nc
How many terms are involved in this contrast? 2
Factor index for No. 1 term is (e.g., 0020): 100
Corresponding coefficient (e.g., 1 or -1): 1
Factor index for No. 2 term is (e.g., 0020): 200
Corresponding coefficient (e.g., 1 or -1): -1
Label for 1st order contrast No. 2 is: S-F
How many terms are involved in this contrast? 2
Factor index for No. 1 term is (e.g., 0020): 010
Corresponding coefficient (e.g., 1 or -1): 1
Factor index for No. 2 term is (e.g., 0020): 020
Corresponding coefficient (e.g., 1 or -1): -1
Done with 1st order contrast information.
2nd order contrasts have 1 factor(s) collapsed.
Notice: Contrasts for random factor are NOT feasible.
How many 2nd-order contrasts? (0 if none) 0
Done with 2nd order contrast information.
3rd order contrasts have 0 factor(s) collapsed.
Notice: Contrasts for random factor are NOT feasible.
How many 3rd-order contrasts? (0 if none) 4
Label for 3rd order contrast No. 1 is: PcS-PncS
How many terms are involved in this contrast? 2
Factor index for No. 1 term is (e.g., 1230): 110
Corresponding coefficient (e.g., 1 or -1): 1
Factor index for No. 2 term is (e.g., 1230): 210
Corresponding coefficient (e.g., 1 or -1): -1
Label for 3rd order contrast No. 2 is: PcF-PncF
How many terms are involved in this contrast? 2
Factor index for No. 1 term is (e.g., 1230): 120
Corresponding coefficient (e.g., 1 or -1): 1
Factor index for No. 2 term is (e.g., 1230): 220
Corresponding coefficient (e.g., 1 or -1): -1
Label for 3rd order contrast No. 3 is: PcS-PcF
How many terms are involved in this contrast? 2
Factor index for No. 1 term is (e.g., 1230): 110
Corresponding coefficient (e.g., 1 or -1): 1
Factor index for No. 2 term is (e.g., 1230): 120
Corresponding coefficient (e.g., 1 or -1): -1
Label for 3rd order contrast No. 4 is: PncS-PncF
How many terms are involved in this contrast? 2
Factor index for No. 1 term is (e.g., 1230): 210
Corresponding coefficient (e.g., 1 or -1): 1
Factor index for No. 2 term is (e.g., 1230): 220
Corresponding coefficient (e.g., 1 or -1): -1
Done with 3rd order contrast information.
??? Reference to non-existent field 'idx3'.
Error in ==> ContrVec at 328
switch Contr.ord3.cnt(i).idx3
Error in ==> PreProc at 352
[err, Contr] = ContrVec(3, n, NF, group, dmat, Contr, FL, num_col);
Error in ==> GroupAna at 1631
[err, Qd, s, termname, nterms, sindices, dfbothSS, modw, modwo, tnames, dfterm, dfe, Contr] =
PreProc(ntot, NF, group, varnames, FL, Contr, cov, unbalanced);
>>
| Subject | Author | Posted |
|---|---|---|
|
Deborah Kerr | March 28, 2010 09:13PM |
|
Gang Chen | March 29, 2010 09:32AM |
|
Deborah Kerr | March 29, 2010 11:00AM |
|
Gang Chen | March 29, 2010 01:04PM |
