3dLME data files could not be loaded

cgodwin9 · July 13, 2018, 6:00am

Hi,

I am trying to run 3dLME on my fmri data, and I’m running into a problem in the beginning where it says my data files cannot be loaded. I’ve come across some similar messages posted on this board, but none of the solutions have helped me so far.

I’ve pasted the output below.

Here is some additional info: I have set up the table in a separate .txt file separate from the script. I checked that formatting was ok in both files and ran “file_tool -test -infiles my_script.txt” to be sure. I can even copy one of the stats filenames directly from the terminal’s error output (e.g., stats.s3+tlrc’[lower_1#0_Coef]') and use it in 3dinfo to obtain the info on the file, so it looks like the filenames work with other commands like 3dinfo. I have also followed the suggestion at the bottom of the output to check the dimensions, but all files have the same dimensions

I greatly appreciate any help with this, thank you!

Sincerely,
Christine

Here is the afni output:

DESKTOP-C9KOHDO:~/desktop/lme_folder> sh group_3dLME_syntax_run.sh
Read 544 items
Loading required package: nlme
Package nlme loaded successfully!

Loading required package: phia
Loading required package: car
Package phia loaded successfully!

++++++++++++++++++++++++++++++++++++++++++++++++++++
***** Summary information of data structure *****
31 subjects : s03 s05 s06 s07 s08 s09 s10 s11 s12 s13 s14 s15 s16 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27 s28 s29 s30 s31 s32 s33 s34 s35
108 response values
2 levels for factor Behav : high low
2 levels for factor Report : off-task on-task
4 post hoc tests

Contingency tables of subject distributions among the categorical variables:

Tabulation of subjects against all categorical variables

Subj vs Behav:

      high low
  s03    2   2
  s05    1   2
  s06    1   2
  s07    1   2
  s08    2   1
  s09    2   2
  s10    2   2
  s11    2   2
  s12    2   2
  s13    2   2
  s14    2   2
  s15    2   1
  s16    1   1
  s18    2   2
  s19    1   2
  s20    2   2
  s21    2   2
  s22    2   2
  s23    2   2
  s24    2   2
  s25    2   2
  s26    2   2
  s27    1   1
  s28    1   1
  s29    2   2
  s30    1   1
  s31    2   2
  s32    1   1
  s33    2   2
  s34    2   2
  s35    2   2

Subj vs Report:

  off-task on-task

s03 2 2
s05 2 1
s06 2 1
s07 2 1
s08 1 2
s09 2 2
s10 2 2
s11 2 2
s12 2 2
s13 2 2
s14 2 2
s15 2 1
s16 2 0
s18 2 2
s19 2 1
s20 2 2
s21 2 2
s22 2 2
s23 2 2
s24 2 2
s25 2 2
s26 2 2
s27 2 0
s28 2 0
s29 2 2
s30 1 1
s31 2 2
s32 2 0
s33 2 2
s34 2 2
s35 2 2
***** End of data structure information *****
++++++++++++++++++++++++++++++++++++++++++++++++++++

Reading input files now…

** ERROR: Dset stats.s3+tlrc’[lower_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s3+tlrc’[lower_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s3+tlrc’[upper_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s3+tlrc’[lower_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s3+tlrc’[upper_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s10+tlrc’[lower_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s10+tlrc’[upper_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s10+tlrc’[lower_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s10+tlrc’[upper_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s11+tlrc’[lower_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s11+tlrc’[upper_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s11+tlrc’[lower_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s11+tlrc’[upper_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s12+tlrc’[lower_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s12+tlrc’[upper_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s12+tlrc’[lower_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s12+tlrc’[upper_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s13+tlrc’[lower_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s13+tlrc’[upper_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s13+tlrc’[lower_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s13+tlrc’[upper_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s14+tlrc’[lower_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s14+tlrc’[upper_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s14+tlrc’[lower_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s14+tlrc’[upper_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s15+tlrc’[upper_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s15+tlrc’[lower_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s15+tlrc’[upper_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s16+tlrc’[lower_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s16+tlrc’[upper_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s18+tlrc’[lower_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s18+tlrc’[upper_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s18+tlrc’[lower_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s18+tlrc’[upper_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s19+tlrc’[lower_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s19+tlrc’[lower_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s19+tlrc’[upper_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s20+tlrc’[lower_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s20+tlrc’[upper_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s20+tlrc’[lower_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s20+tlrc’[upper_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s21+tlrc’[lower_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s21+tlrc’[upper_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s21+tlrc’[lower_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s21+tlrc’[upper_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s22+tlrc’[lower_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s22+tlrc’[upper_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s22+tlrc’[lower_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s22+tlrc’[upper_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s23+tlrc’[lower_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s23+tlrc’[upper_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s23+tlrc’[lower_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s23+tlrc’[upper_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s24+tlrc’[lower_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s24+tlrc’[upper_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s24+tlrc’[lower_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s24+tlrc’[upper_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s25+tlrc’[lower_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s25+tlrc’[upper_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s25+tlrc’[lower_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s25+tlrc’[upper_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s26+tlrc’[lower_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s26+tlrc’[upper_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s26+tlrc’[lower_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s26+tlrc’[upper_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s27+tlrc’[lower_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s27+tlrc’[upper_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s28+tlrc’[lower_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s28+tlrc’[upper_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s29+tlrc’[lower_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s29+tlrc’[upper_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s29+tlrc’[lower_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s29+tlrc’[upper_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s30+tlrc’[lower_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s30+tlrc’[upper_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s31+tlrc’[lower_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s31+tlrc’[upper_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s31+tlrc’[lower_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s31+tlrc’[upper_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s32+tlrc’[lower_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s32+tlrc’[upper_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s33+tlrc’[lower_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s33+tlrc’[upper_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s33+tlrc’[lower_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s33+tlrc’[upper_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s34+tlrc’[lower_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s34+tlrc’[upper_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s34+tlrc’[lower_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s34+tlrc’[upper_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s35+tlrc’[lower_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s35+tlrc’[upper_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s35+tlrc’[lower_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s35+tlrc’[upper_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s5+tlrc’[lower_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s5+tlrc’[lower_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s5+tlrc’[upper_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s6+tlrc’[lower_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s6+tlrc’[lower_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s6+tlrc’[upper_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s7+tlrc’[lower_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s7+tlrc’[lower_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s7+tlrc’[upper_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s8+tlrc’[lower_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s8+tlrc’[upper_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s8+tlrc’[upper_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s9+tlrc’[lower_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s9+tlrc’[upper_1#0_Coef]’ could not be loaded
** ERROR: Dset stats.s9+tlrc’[lower_3#0_Coef]’ could not be loaded
** ERROR: Dset stats.s9+tlrc’[upper_3#0_Coef]’ could not be loaded

** Error:
At least one of the input files has different dimensions!
Run “3dinfo -header_line -prefix -same_grid -n4 *.HEAD” in the directory where
the files are stored, and pinpoint out which file(s) is the trouble maker.
Replace *.HEAD with *.nii or something similar for other file formats.

Gang · July 13, 2018, 10:03pm

Are you sure those files are in the directory where you run the 3dLME script? If so, in the directory where you run your 3dLME script, what do you get when you try the following at the terminal?

3dinfo stats.s3+tlrc’[lower_1#0_Coef]’

cgodwin9 · July 16, 2018, 4:13am

Thank you – yes, they are all in the same folder. Here is the output when I run 3dinfo

DESKTOP-C9KOHDO:~/desktop/lme_folder> 3dinfo stats.s3+tlrc’[lower_1#0_Coef]’
++ 3dinfo: AFNI version=AFNI_18.2.04 (Jul 6 2018) [64-bit]

Dataset File: stats.s3+tlrc
Identifier Code: XYZ_PXgDS-ug8Ee2OavVhX1jZw Creation Date: Fri Mar 2 12:41:30 2018
Template Space: MNI
Dataset Type: Func-Bucket (-fbuc)
Byte Order: LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode: BRIK
Storage Space: 1,086,532 (1.1 million [mega]) bytes
Geometry String: “MATRIX(-3,0,0,90,0,-3,0,126,0,0,3,-72):61,73,61”
Data Axes Tilt: Plumb
Data Axes Orientation:
first (x) = Left-to-Right
second (y) = Posterior-to-Anterior
third (z) = Inferior-to-Superior [-orient LPI]
R-to-L extent: -90.000 [R] -to- 90.000 [L] -step- 3.000 mm [ 61 voxels]
A-to-P extent: -90.000 [A] -to- 126.000 [P] -step- 3.000 mm [ 73 voxels]
I-to-S extent: -72.000 [I] -to- 108.000 [S] -step- 3.000 mm [ 61 voxels]
Number of values stored at each pixel = 1
– At sub-brick #0 ‘lower_1#0_Coef’ datum type is float: -3.93021 to 1.91243