AFNI version info (afni -ver): Precompiled binary macos_10.12_local: Oct 31 2024 (Version AFNI_24.3.06 'Elagabalus')
Hi everyone,
Thanks for taking the time to read my post.
I'm encountering an issue where AFNI isn’t “reading” my datasets during a 3dMVM analysis. My script runs to completion and produces output files, but when I visualize the results, there is no statistically significant signal—everything is zero. Upon checking the error logs, several of my datasets are not being recognized (displaying “NO-DSET” errors).
Here’s what I’ve done so far:
I verified that all file paths are correct and that I have the proper read privileges.
I confirmed that the necessary datasets (paired .BRIK/.HEAD files) exist in their respective session folders.
I converted the datasets to NIfTI and used quotes around the file paths, but AFNI still fails to recognize them.
If anyone has encountered a similar problem or has any insight into why AFNI might be returning “NO-DSET” errors despite valid file paths, I would greatly appreciate your advice.
Thanks in advance for your help!
Notes: I am amare that some sessions are missing (movement) and that the files gained an extra 'sub' on the front!
Data Table:
Subj Sex Age Years_OpioidUse Years_StimulantUse Time InputFile
520 M 34 18 16 ses-00 /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-00/sub-sub-520-CPO-ses-00_seed_corr_z+tlrc
520 M 34 18 16 ses-07 /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-07/sub-sub-520-CPO-ses-07_seed_corr_z+tlrc
520 M 34 18 16 ses-30 /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-30/sub-sub-520-CPO-ses-30_seed_corr_z+tlrc
521 M 45 8 13 ses-07 /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-07/sub-sub-521-CPO-ses-07_seed_corr_z+tlrc
521 M 45 8 13 ses-30 /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-30/sub-sub-521-CPO-ses-30_seed_corr_z+tlrc
522 M 32 7 13 ses-00 /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-00/sub-sub-522-CPO-ses-00_seed_corr_z+tlrc
522 M 32 7 13 ses-30 /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-30/sub-sub-522-CPO-ses-30_seed_corr_z+tlrc
523 M 55 0 40 ses-00 /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-00/sub-sub-523-CPO-ses-00_seed_corr_z+tlrc
524 M 49 29 10 ses-07 /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-07/sub-sub-524-CPO-ses-07_seed_corr_z+tlrc
524 M 49 29 10 ses-30 /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-30/sub-sub-524-CPO-ses-30_seed_corr_z+tlrc
525 F 32 4 8 ses-00 /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-00/sub-sub-525-CPO-ses-00_seed_corr_z+tlrc
525 F 32 4 8 ses-07 /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-07/sub-sub-525-CPO-ses-07_seed_corr_z+tlrc
525 F 32 4 8 ses-30 /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-30/sub-sub-525-CPO-ses-30_seed_corr_z+tlrc
526 F 31 14 10 ses-00 /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-00/sub-sub-526-CPO-ses-00_seed_corr_z+tlrc
526 F 31 14 10 ses-07 /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-07/sub-sub-526-CPO-ses-07_seed_corr_z+tlrc
526 F 31 14 10 ses-30 /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-30/sub-sub-526-CPO-ses-30_seed_corr_z+tlrc
527 M 32 13 12 ses-00 /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-00/sub-sub-527-CPO-ses-00_seed_corr_z+tlrc
527 M 32 13 12 ses-07 /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-07/sub-sub-527-CPO-ses-07_seed_corr_z+tlrc
528 F 24 6 6 ses-07 /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-07/sub-sub-528-CPO-ses-07_seed_corr_z+tlrc
529 F 22 5 0 ses-00 /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-00/sub-sub-529-CPO-ses-00_seed_corr_z+tlrc
529 F 22 5 0 ses-07 /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-07/sub-sub-529-CPO-ses-07_seed_corr_z+tlrc
529 F 22 5 0 ses-30 /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-30/sub-sub-529-CPO-ses-30_seed_corr_z+tlrc
530 M 32 3 11 ses-00 /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-00/sub-sub-530-CPO-ses-00_seed_corr_z+tlrc
530 M 32 3 11 ses-07 /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-07/sub-sub-530-CPO-ses-07_seed_corr_z+tlrc
530 M 32 3 11 ses-30 /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-30/sub-sub-530-CPO-ses-30_seed_corr_z+tlrc
3dMVM script:
3dMVM -prefix GroupxTime_FC \
-jobs 4 \
-bsVars "Sex+Age+Years_OpioidUse+Years_StimulantUse" \
-wsVars "Time" \
-qVars "Age,Years_OpioidUse,Years_StimulantUse" \
-dataTable @3dMVM_final.txt
**Error 1**: bekahthurn@HSC-C02TV1J4HTD8:~/Desktop$ ./3dMVM_script.sh
Checking dataTable file:
3dMVM_final.txt
++Good: Table is regular and rectangular.
Read 182 items
Dimensions:
rows: 25 | columns: 7
+* Warning: Each "Subj" does not have the same number of "InputFiles"!
Most Subj have 3 InputFiles. The following Subj differ:
Subj NumInputFiles
521 2
522 2
523 1
524 2
527 2
528 1
Data summary:
Variable Detected_Type Details
Subj Subjects Num Subjects=11
Sex Categorical Counts: F=10 | M=15
Age Quantitative Min=22 | Max=55 | Num outliers=9
Years_OpioidUse Quantitative Min=0 | Max=29
Years_StimulantUse Quantitative Min=0 | Max=40 | Num outliers=4
Time Categorical Counts: ses-00=8 | ses-07=9 | ses-30=8
InputFile Data Number of InputFiles=25
++ Good: All InputFiles exist.
++ Good: All InputFiles have exactly 1 volume.
++ Good: All InputFiles are on the same grid.
+* Warning: Log file: ./GroupxTime_FC_log.txt exists! NOT OVERWRITING!! - *this was corrected*
Warning message:
In readLines(file.in) : incomplete final line found on '3dMVM_final.txt'
Loading required package: lme4
Loading required package: Matrix
************
Welcome to afex. For support visit: http://afex.singmann.science/
- Functions for ANOVAs: aov_car(), aov_ez(), and aov_4()
- Methods for calculating p-values with mixed(): 'S', 'KR', 'LRT', and 'PB'
- 'afex_aov' and 'mixed' objects can be passed to emmeans() for follow-up tests
- Get and set global package options with: afex_options()
- Set sum-to-zero contrasts globally: set_sum_contrasts()
- For example analyses see: browseVignettes("afex")
************
Attaching package: ‘afex’
The following object is masked from ‘package:lme4’:
lmer
Loading required package: car
Loading required package: carData
++++++++++++++++++++++++++++++++++++++++++++++++++++
***** Summary information of data structure *****
11 subjects : 520 521 522 523 524 525 526 527 528 529 530
25 response values
2 levels for factor Sex : F M
25 centered values for numeric variable Age : 0.08 0.08 0.08 11.08 11.08 -1.92 -1.92 21.08 15.08 15.08 -1.92 -1.92 -1.92 -2.92 -2.92 -2.92 -1.92 -1.92 -9.92 -11.92 -11.92 -11.92 -1.92 -1.92 -1.92
25 centered values for numeric variable Years_OpioidUse : 7.92 7.92 7.92 -2.08 -2.08 -3.08 -3.08 -10.08 18.92 18.92 -6.08 -6.08 -6.08 3.92 3.92 3.92 2.92 2.92 -4.08 -5.08 -5.08 -5.08 -7.08 -7.08 -7.08
25 centered values for numeric variable Years_StimulantUse : 4.92 4.92 4.92 1.92 1.92 1.92 1.92 28.92 -1.08 -1.08 -3.08 -3.08 -3.08 -1.08 -1.08 -1.08 0.92 0.92 -5.08 -11.08 -11.08 -11.08 -0.08 -0.08 -0.08
3 levels for factor Time : ses-00 ses-07 ses-30
0 post hoc tests
Contingency tables of subject distributions among the categorical variables:
Time
Sex ses-00 ses-07 ses-30
F 3 4 3
M 5 5 5
Tabulation of subjects against each of the categorical variables:
~~~~~~~~~~~~~~
lop$nSubj vs Sex:
F M
520 0 3
521 0 2
522 0 2
523 0 1
524 0 2
525 3 0
526 3 0
527 0 2
528 1 0
529 3 0
530 0 3
~~~~~~~~~~~~~~
lop$nSubj vs Time:
ses-00 ses-07 ses-30
520 1 1 1
521 0 1 1
522 1 0 1
523 1 0 0
524 0 1 1
525 1 1 1
526 1 1 1
527 1 1 0
528 0 1 0
529 1 1 1
530 1 1 1
***** End of data structure information *****
++++++++++++++++++++++++++++++++++++++++++++++++++++
Reading input files now...
Reading input files: Done!
Range of input data: [-0.633, 0.954]
If the program hangs here for more than, for example, half an hour,
kill the process because the model specification or the GLT coding
is likely inappropriate.
[1] "Great, test run passed at voxel (25, 46, 38)!"
[1] "Start to compute 77 slices along Z axis. You can monitor the progress"
[1] "and estimate the total run time as shown below."
[1] "03/02/25 13:57:03.891"
Loading required package: snow
Package snow loaded successfully!
Z slice 1 done: 03/02/25 13:57:10.849
Z slice 2 done: 03/02/25 13:57:10.902
Z slice 3 done: 03/02/25 13:57:11.255
Z slice 4 done: 03/02/25 13:57:12.121
Z slice 5 done: 03/02/25 13:57:13.676
Z slice 6 done: 03/02/25 13:57:17.369
Z slice 7 done: 03/02/25 13:57:27.339
Z slice 8 done: 03/02/25 13:57:44.712
Z slice 9 done: 03/02/25 13:58:05.836
Z slice 10 done: 03/02/25 13:58:26.101
Z slice 11 done: 03/02/25 13:58:47.055
Z slice 12 done: 03/02/25 13:59:10.472
Z slice 13 done: 03/02/25 13:59:35.208
Z slice 14 done: 03/02/25 14:00:03.675
Z slice 15 done: 03/02/25 14:00:33.364
Z slice 16 done: 03/02/25 14:01:07.217
Z slice 17 done: 03/02/25 14:01:40.928
Z slice 18 done: 03/02/25 14:02:16.950
Z slice 19 done: 03/02/25 14:02:52.903
Z slice 20 done: 03/02/25 14:03:30.541
Z slice 21 done: 03/02/25 14:04:13.264
Z slice 22 done: 03/02/25 14:04:55.462
Z slice 23 done: 03/02/25 14:05:39.062
Z slice 24 done: 03/02/25 14:06:24.167
Z slice 25 done: 03/02/25 14:07:10.144
Z slice 26 done: 03/02/25 14:07:57.672
Z slice 27 done: 03/02/25 14:08:46.875
Z slice 28 done: 03/02/25 14:09:35.023
Z slice 29 done: 03/02/25 14:10:23.702
Z slice 30 done: 03/02/25 14:11:12.544
Z slice 31 done: 03/02/25 14:12:00.937
Z slice 32 done: 03/02/25 14:12:49.357
Z slice 33 done: 03/02/25 14:13:38.103
Z slice 34 done: 03/02/25 14:14:26.589
Z slice 35 done: 03/02/25 14:15:15.167
Z slice 36 done: 03/02/25 14:16:03.575
Z slice 37 done: 03/02/25 14:16:51.612
Z slice 38 done: 03/02/25 14:17:39.352
Z slice 39 done: 03/02/25 14:18:26.674
Z slice 40 done: 03/02/25 14:19:13.362
Z slice 41 done: 03/02/25 14:19:59.934
Z slice 42 done: 03/02/25 14:20:46.366
Z slice 43 done: 03/02/25 14:21:32.484
Z slice 44 done: 03/02/25 14:22:17.819
Z slice 45 done: 03/02/25 14:23:02.779
Z slice 46 done: 03/02/25 14:23:47.016
Z slice 47 done: 03/02/25 14:24:30.937
Z slice 48 done: 03/02/25 14:25:13.801
Z slice 49 done: 03/02/25 14:25:55.901
Z slice 50 done: 03/02/25 14:26:36.471
Z slice 51 done: 03/02/25 14:27:16.647
Z slice 52 done: 03/02/25 14:27:55.036
Z slice 53 done: 03/02/25 14:28:31.656
Z slice 54 done: 03/02/25 14:29:05.698
Z slice 55 done: 03/02/25 14:29:37.685
Z slice 56 done: 03/02/25 14:30:06.660
Z slice 57 done: 03/02/25 14:30:34.224
Z slice 58 done: 03/02/25 14:30:58.438
Z slice 59 done: 03/02/25 14:31:20.534
Z slice 60 done: 03/02/25 14:31:38.216
Z slice 61 done: 03/02/25 14:31:53.464
Z slice 62 done: 03/02/25 14:32:03.889
Z slice 63 done: 03/02/25 14:32:11.166
Z slice 64 done: 03/02/25 14:32:13.619
Z slice 65 done: 03/02/25 14:32:13.668
Z slice 66 done: 03/02/25 14:32:13.733
Z slice 67 done: 03/02/25 14:32:13.780
Z slice 68 done: 03/02/25 14:32:13.834
Z slice 69 done: 03/02/25 14:32:13.881
Z slice 70 done: 03/02/25 14:32:13.931
Z slice 71 done: 03/02/25 14:32:13.979
Z slice 72 done: 03/02/25 14:32:14.029
Z slice 73 done: 03/02/25 14:32:14.077
Z slice 74 done: 03/02/25 14:32:14.128
Z slice 75 done: 03/02/25 14:32:14.175
Z slice 76 done: 03/02/25 14:32:14.226
Z slice 77 done: 03/02/25 14:32:14.284
*+ WARNING: mri_fdrize: will not process only 0 values (min=20)
++ Smallest FDR q [0 (Intercept) F] = 0
*+ WARNING: mri_fdrize: will not process only 0 values (min=20)
++ Smallest FDR q [1 Sex F] = 0
*+ WARNING: mri_fdrize: will not process only 0 values (min=20)
++ Smallest FDR q [2 Age F] = 0
*+ WARNING: mri_fdrize: will not process only 0 values (min=20)
++ Smallest FDR q [3 Years_OpioidUse F] = 0
*+ WARNING: mri_fdrize: will not process only 0 values (min=20)
++ Smallest FDR q [4 Years_StimulantUse F] = 0
*+ WARNING: mri_fdrize: will not process only 0 values (min=20)
++ Smallest FDR q [5 Time F] = 0
*+ WARNING: mri_fdrize: will not process only 0 values (min=20)
++ Smallest FDR q [6 Sex:Time F] = 0
*+ WARNING: mri_fdrize: will not process only 0 values (min=20)
++ Smallest FDR q [7 Age:Time F] = 0
*+ WARNING: mri_fdrize: will not process only 0 values (min=20)
++ Smallest FDR q [8 Years_OpioidUse:Time F] = 0
*+ WARNING: mri_fdrize: will not process only 0 values (min=20)
++ Smallest FDR q [9 Years_StimulantUse:Time F] = 0
Congratulations! You have got an output GroupxTime_FC+tlrc.
Warning messages:
1: Missing values for 6 ID(s), which were removed before analysis:
521, 522, 523, 524, 527, 528
Below the first few rows (in wide format) of the removed cases with missing data.
Subj Sex Age Years_OpioidUse Years_StimulantUse ses.00 ses.07 ses.30
# 2 521 M 11.08 -2.08 1.92 NaN 0.023209488 0.17367652
# 3 522 M -1.92 -3.08 1.92 -0.03544143 NaN 0.13412245
# 4 523 M 21.08 -10.08 28.92 0.09559521 NaN NaN
# 5 524 M 15.08 18.92 -1.08 NaN 0.074980572 0.06141484
# 8 527 M -1.92 2.92 0.92 0.14174999 0.005246514 NaN
# 9 528 F -9.92 -4.08 -5.08 NaN 0.026811861 NaN
2: In summary.Anova.mlm(object$Anova, multivariate = FALSE) :
one or more error SSP matrix:
corresponding non-sphericity tests and corrections not available
(base) bekahthurn@HSC-C02TV1J4HTD8:~/Desktop$
~~~~~~~~~~~~~~~~~~~~~~~~~~~
errorlog: temp
Sun Mar 2 13:42:36 2025
Checking dataTable file:
3dMVM_final.txt
++Good: Table is regular and rectangular.
Dimensions:
rows: 26 | columns: 7
+* Warning: Each "Subj" does not have the same number of "InputFiles"!
Most Subj have 3 InputFiles. The following Subj differ:
Subj NumInputFiles
521 2
522 2
523 1
524 2
528 1
Data summary:
Variable Detected_Type Details
Subj Subjects Num Subjects=11
Sex Categorical Counts: F=10 | M=16
Age Quantitative Min=22 | Max=55 | Num outliers=9
Years_OpioidUse Quantitative Min=0 | Max=29
Years_StimulantUse Quantitative Min=0 | Max=40 | Num outliers=4
Time Categorical Counts: ses-00=8 | ses-07=9 | ses-30=9
InputFile Data Number of InputFiles=26
** ERROR: Datasets not found!!!
[1] /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-00/sub-sub-520-CPO-ses-00_seed_corr_z+tlrc+tlrc
[2] /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-07/sub-sub-520-CPO-ses-07_seed_corr_z+tlrc+tlrc
[3] /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-30/sub-sub-520-CPO-ses-30_seed_corr_z+tlrc+tlrc
[4] /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-07/sub-sub-521-CPO-ses-07_seed_corr_z+tlrc+tlrc
[5] /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-30/sub-sub-521-CPO-ses-30_seed_corr_z+tlrc+tlrc
[6] /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-00/sub-sub-522-CPO-ses-00_seed_corr_z+tlrc+tlrc
[7] /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-30/sub-sub-522-CPO-ses-30_seed_corr_z+tlrc+tlrc
[8] /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-00/sub-sub-523-CPO-ses-00_seed_corr_z+tlrc+tlrc
[9] /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-07/sub-sub-524-CPO-ses-07_seed_corr_z+tlrc+tlrc
[10] /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-30/sub-sub-524-CPO-ses-30_seed_corr_z+tlrc+tlrc
[11] /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-00/sub-sub-525-CPO-ses-00_seed_corr_z+tlrc+tlrc
[12] /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-07/sub-sub-525-CPO-ses-07_seed_corr_z+tlrc+tlrc
[13] /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-30/sub-sub-525-CPO-ses-30_seed_corr_z+tlrc+tlrc
[14] /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-00/sub-sub-526-CPO-ses-00_seed_corr_z+tlrc+tlrc
[15] /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-07/sub-sub-526-CPO-ses-07_seed_corr_z+tlrc+tlrc
[16] /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-30/sub-sub-526-CPO-ses-30_seed_corr_z+tlrc+tlrc
[17] /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-00/sub-sub-527-CPO-ses-00_seed_corr_z+tlrc+tlrc
[18] /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-07/sub-sub-527-CPO-ses-07_seed_corr_z+tlrc+tlrc
[19] /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-30/sub-sub-527-CPO-ses-30_seed_corr_z+tlrc+tlrc
[20] /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-07/sub-sub-528-CPO-ses-07_seed_corr_z+tlrc+tlrc
[21] /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-00/sub-sub-529-CPO-ses-00_seed_corr_z+tlrc+tlrc
[22] /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-07/sub-sub-529-CPO-ses-07_seed_corr_z+tlrc+tlrc
[23] /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-30/sub-sub-529-CPO-ses-30_seed_corr_z+tlrc+tlrc
[24] /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-00/sub-sub-530-CPO-ses-00_seed_corr_z+tlrc+tlrc
[25] /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-07/sub-sub-530-CPO-ses-07_seed_corr_z+tlrc+tlrc
[26] /Volumes/EHD/CPO_DATA/RS_NAc_1/Ses-30/sub-sub-530-CPO-ses-30_seed_corr_z+tlrc+tlrc
** ERROR: One or more tests failed. See above!!!
(base) bekahthurn@HSC-C02TV1J4HTD8:~/Desktop$ 3dinfo -min -max GroupxTime_FC+tlrc
0|0|0|0|0|0|0|0|0|0 0|0|0|0|0|0|0|0|0|0
base) bekahthurn@HSC-C02TV1J4HTD8:~/Desktop$ 3dinfo -min -max $(awk '{print $NF}' 3dMVM_final.txt | tail -n +2)
NO-DSET NO-DSET
NO-DSET NO-DSET
NO-DSET NO-DSET
NO-DSET NO-DSET
NO-DSET NO-DSET
NO-DSET NO-DSET
NO-DSET NO-DSET
NO-DSET NO-DSET
NO-DSET NO-DSET
NO-DSET NO-DSET
NO-DSET NO-DSET
NO-DSET NO-DSET
NO-DSET NO-DSET
NO-DSET NO-DSET
NO-DSET NO-DSET
NO-DSET NO-DSET
NO-DSET NO-DSET
NO-DSET NO-DSET
NO-DSET NO-DSET
NO-DSET NO-DSET
NO-DSET NO-DSET
NO-DSET NO-DSET
NO-DSET NO-DSET
NO-DSET NO-DSET
-0.259665 0.605048