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.
