3dLME: Error: "At least one of the input files has different dimensions!"

sophia · May 26, 2017, 4:37pm

I ran 3dLME (2 repeated scans; 2 groups), but input files could not be uploaded, with the following error:
“At least one of the input files has different dimensions!”

Then, I ran 3dinfo -header_line -prefix -same_grid -n4 *.HEAD, which yielded the output as follows:

          prefix	=grid?	Ni	Nj	Nk	Nv
      DBD_A00_r1	1	91	109	91	1
      DBD_A00_r2	1	91	109	91	1
      DBD_A01_r1	1	91	109	91	1
      DBD_A01_r2	1	91	109	91	1
      DBD_A02_r1	1	91	109	91	1
      DBD_A02_r2	1	91	109	91	1
      .
      .
     (For all subjects, n = 28, the pattern above can be seen)

To me, no file had different dimensions. What are problems here? Your guidance/suggestion is appreciated!

Best,
Sophia

Gang · May 26, 2017, 7:05pm

Sophia,

What is you AFNI version?

afni -ver

If not current, update it:

@update.afni.binaries -d

and see if that fixes the problem.

sophia · May 26, 2017, 7:16pm

Hi Gang , thanks for your quick email.

afni -ver
Precompiled binary macosx_10.7_local: May 21 2017 (Version AFNI_17.1.06): this is the AFNI version I used.
The same error was given when I ran it on the lab’s server using Version AFNI_16.2.16.

Below is the output on the terminal when I ran 3dLME.txt. I wonder if I made some errors in the setting. Any idea? Many thanks in advance.
Sophia

Output on the terminal

sh -x mk_3dLME.txt

3dLME -prefix DBD_adult -model ‘condgroup’ -mask group_mask_to_standard_2mm_gm_25pc_all_28_R1.nii.gz -ranEff ‘~1’ -SS_type 3 -num_glt 2 -gltLabel 1 r1-r2 -gltCode 1 'cond : 1r1 -1r2’ -gltLabel 2 ag_r1-r2 -gltCode 2 'cond : 1r1 -1r2 group : 1ag’ -num_glf 1 -glfLabel 1 r1-r2 -glfCode 1 ‘group : 1ctr & 1ag cond : 1r1 -1r2’ -dataTable Subj cond group InputFile DBD_A00 r1 ag ‘DBD_A00_r1+tlrc[r1#0_Coef]’ DBD_A00 r2 ag ‘DBD_A00_r2+tlrc[r2#0_Coef]’ DBD_A03 r1 ag ‘DBD_A03_r1+tlrc[r1#0_Coef]’ DBD_A03 r2 ag ‘DBD_A03_r2+tlrc[r2#0_Coef]’ DBD_A05 r1 ag ‘DBD_A05_r1+tlrc[r1#0_Coef]’ DBD_A05 r2 ag ‘DBD_A05_r2+tlrc[r2#0_Coef]’ DBD_A06 r1 ag ‘DBD_A06_r1+tlrc[r1#0_Coef]’ DBD_A06 r2 ag ‘DBD_A06_r2+tlrc[r2#0_Coef]’ DBD_A07 r1 ag ‘DBD_A07_r1+tlrc[r1#0_Coef]’ DBD_A07 r2 ag ‘DBD_A07_r2+tlrc[r2#0_Coef]’ DBD_A08 r1 ag ‘DBD_A08_r1+tlrc[r1#0_Coef]’ DBD_A08 r2 ag ‘DBD_A08_r2+tlrc[r2#0_Coef]’ DBD_A10 r1 ag ‘DBD_A10_r1+tlrc[r1#0_Coef]’ DBD_A10 r2 ag ‘DBD_A10_r2+tlrc[r2#0_Coef]’ DBD_A11 r1 ag ‘DBD_A11_r1+tlrc[r1#0_Coef]’ DBD_A11 r2 ag ‘DBD_A11_r2+tlrc[r2#0_Coef]’ DBD_A15 r1 ag ‘DBD_A15_r1+tlrc[r1#0_Coef]’ DBD_A15 r2 ag ‘DBD_A15_r2+tlrc[r2#0_Coef]’ DBD_A20 r1 ag ‘DBD_A20_r1+tlrc[r1#0_Coef]’ DBD_A20 r2 ag ‘DBD_A20_r2+tlrc[r2#0_Coef]’ DBD_A21 r1 ag ‘DBD_A21_r1+tlrc[r1#0_Coef]’ DBD_A21 r2 ag ‘DBD_A21_r2+tlrc[r2#0_Coef]’ DBD_A22 r1 ag ‘DBD_A22_r1+tlrc[r1#0_Coef]’ DBD_A22 r2 ag ‘DBD_A22_r2+tlrc[r2#0_Coef]’ DBD_A23 r1 ag ‘DBD_A23_r1+tlrc[r1#0_Coef]’ DBD_A23 r2 ag ‘DBD_A23_r2+tlrc[r2#0_Coef]’ DBD_A24 r1 ag ‘DBD_A24_r1+tlrc[r1#0_Coef]’ DBD_A24 r2 ag ‘DBD_A24_r2+tlrc[r2#0_Coef]’ DBD_A25 r1 ag ‘DBD_A25_r1+tlrc[r1#0_Coef]’ DBD_A25 r2 ag ‘DBD_A25_r2+tlrc[r2#0_Coef]’ DBD_A26 r1 ag ‘DBD_A26_r1+tlrc[r1#0_Coef]’ DBD_A26 r2 ag ‘DBD_A26_r2+tlrc[r2#0_Coef]’ DBD_A27 r1 ag ‘DBD_A27_r1+tlrc[r1#0_Coef]’ DBD_A27 r2 ag ‘DBD_A27_r2+tlrc[r2#0_Coef]’ DBD_A28 r1 ag ‘DBD_A28_r1+tlrc[r1#0_Coef]’ DBD_A28 r2 ag ‘DBD_A28_r2+tlrc[r2#0_Coef]’ DBD_A01 r1 ctr ‘DBD_A01_r1+tlrc[r1#0_Coef]’ DBD_A01 r2 ctr ‘DBD_A01_r2+tlrc[r2#0_Coef]’ DBD_A02 r1 ctr ‘DBD_A02_r1+tlrc[r1#0_Coef]’ DBD_A02 r2 ctr ‘DBD_A02_r2+tlrc[r2#0_Coef]’ DBD_A04 r1 ctr ‘DBD_A04_r1+tlrc[r1#0_Coef]’ DBD_A04 r2 ctr ‘DBD_A04_r2+tlrc[r2#0_Coef]’ DBD_A09 r1 ctr ‘DBD_A09_r1+tlrc[r1#0_Coef]’ DBD_A09 r2 ctr ‘DBD_A09_r2+tlrc[r2#0_Coef]’ DBD_A12 r1 ctr ‘DBD_A12_r1+tlrc[r1#0_Coef]’ DBD_A12 r2 ctr ‘DBD_A12_r2+tlrc[r2#0_Coef]’ DBD_A14 r1 ctr ‘DBD_A14_r1+tlrc[r1#0_Coef]’ DBD_A14 r2 ctr ‘DBD_A14_r2+tlrc[r2#0_Coef]’ DBD_A16 r1 ctr ‘DBD_A16_r1+tlrc[r1#0_Coef]’ DBD_A16 r2 ctr ‘DBD_A16_r2+tlrc[r2#0_Coef]’ DBD_A17 r1 ctr ‘DBD_A17_r1+tlrc[r1#0_Coef]’ DBD_A17 r2 ctr ‘DBD_A17_r2+tlrc[r2#0_Coef]’ DBD_A18 r1 ctr ‘DBD_A18_r1+tlrc[r1#0_Coef]’ DBD_A18 r2 ctr ‘DBD_A18_r2+tlrc[r2#0_Coef]’ DBD_A19 r1 ctr ‘DBD_A19_r1+tlrc[r1#0_Coef]’ DBD_A19 r2 ctr ‘DBD_A19_r2+tlrc[r2#0_Coef]’
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 *****
28 subjects : DBD_A00 DBD_A01 DBD_A02 DBD_A03 DBD_A04 DBD_A05 DBD_A06 DBD_A07 DBD_A08 DBD_A09 DBD_A10 DBD_A11 DBD_A12 DBD_A14 DBD_A15 DBD_A16 DBD_A17 DBD_A18 DBD_A19 DBD_A20 DBD_A21 DBD_A22 DBD_A23 DBD_A24 DBD_A25 DBD_A26 DBD_A27 DBD_A28
56 response values
2 levels for factor cond : r1 r2
2 levels for factor group : ag ctr
2 post hoc tests

Contingency tables of subject distributions among the categorical variables:

Tabulation of subjects against all categorical variables

Subj vs cond:
         
          r1 r2
  DBD_A00  1  1
  DBD_A01  1  1
  DBD_A02  1  1
  DBD_A03  1  1
  DBD_A04  1  1
  DBD_A05  1  1
  DBD_A06  1  1
  DBD_A07  1  1
  DBD_A08  1  1
  DBD_A09  1  1
  DBD_A10  1  1
  DBD_A11  1  1
  DBD_A12  1  1
  DBD_A14  1  1
  DBD_A15  1  1
  DBD_A16  1  1
  DBD_A17  1  1
  DBD_A18  1  1
  DBD_A19  1  1
  DBD_A20  1  1
  DBD_A21  1  1
  DBD_A22  1  1
  DBD_A23  1  1
  DBD_A24  1  1
  DBD_A25  1  1
  DBD_A26  1  1
  DBD_A27  1  1
  DBD_A28  1  1

Subj vs group:

      ag ctr

DBD_A00 2 0
DBD_A01 0 2
DBD_A02 0 2
DBD_A03 2 0
DBD_A04 0 2
DBD_A05 2 0
DBD_A06 2 0
DBD_A07 2 0
DBD_A08 2 0
DBD_A09 0 2
DBD_A10 2 0
DBD_A11 2 0
DBD_A12 0 2
DBD_A14 0 2
DBD_A15 2 0
DBD_A16 0 2
DBD_A17 0 2
DBD_A18 0 2
DBD_A19 0 2
DBD_A20 2 0
DBD_A21 2 0
DBD_A22 2 0
DBD_A23 2 0
DBD_A24 2 0
DBD_A25 2 0
DBD_A26 2 0
DBD_A27 2 0
DBD_A28 2 0
***** End of data structure information *****
++++++++++++++++++++++++++++++++++++++++++++++++++++

Reading input files now…

** ERROR: Dset DBD_A00_r1+tlrc[r1#0_Coef] could not be loaded
** ERROR: Dset DBD_A00_r1+tlrc[r1#0_Coef] could not be loaded
** ERROR: Dset DBD_A00_r2+tlrc[r2#0_Coef] could not be loaded
** ERROR: Dset DBD_A03_r1+tlrc[r1#0_Coef] could not be loaded
** ERROR: Dset DBD_A03_r2+tlrc[r2#0_Coef] could not be loaded
** ERROR: Dset DBD_A05_r1+tlrc[r1#0_Coef] could not be loaded
** ERROR: Dset DBD_A05_r2+tlrc[r2#0_Coef] could not be loaded
** ERROR: Dset DBD_A06_r1+tlrc[r1#0_Coef] could not be loaded
** ERROR: Dset DBD_A06_r2+tlrc[r2#0_Coef] could not be loaded
** ERROR: Dset DBD_A07_r1+tlrc[r1#0_Coef] could not be loaded
** ERROR: Dset DBD_A07_r2+tlrc[r2#0_Coef] could not be loaded
** ERROR: Dset DBD_A08_r1+tlrc[r1#0_Coef] could not be loaded
** ERROR: Dset DBD_A08_r2+tlrc[r2#0_Coef] could not be loaded
** ERROR: Dset DBD_A10_r1+tlrc[r1#0_Coef] could not be loaded
** ERROR: Dset DBD_A10_r2+tlrc[r2#0_Coef] could not be loaded
** ERROR: Dset DBD_A11_r1+tlrc[r1#0_Coef] could not be loaded
** ERROR: Dset DBD_A11_r2+tlrc[r2#0_Coef] could not be loaded
** ERROR: Dset DBD_A15_r1+tlrc[r1#0_Coef] could not be loaded
** ERROR: Dset DBD_A15_r2+tlrc[r2#0_Coef] could not be loaded
** ERROR: Dset DBD_A20_r1+tlrc[r1#0_Coef] could not be loaded
** ERROR: Dset DBD_A20_r2+tlrc[r2#0_Coef] could not be loaded
** ERROR: Dset DBD_A21_r1+tlrc[r1#0_Coef] could not be loaded
** ERROR: Dset DBD_A21_r2+tlrc[r2#0_Coef] could not be loaded
** ERROR: Dset DBD_A22_r1+tlrc[r1#0_Coef] could not be loaded
** ERROR: Dset DBD_A22_r2+tlrc[r2#0_Coef] could not be loaded
** ERROR: Dset DBD_A23_r1+tlrc[r1#0_Coef] could not be loaded
** ERROR: Dset DBD_A23_r2+tlrc[r2#0_Coef] could not be loaded
** ERROR: Dset DBD_A24_r1+tlrc[r1#0_Coef] could not be loaded
** ERROR: Dset DBD_A24_r2+tlrc[r2#0_Coef] could not be loaded
** ERROR: Dset DBD_A25_r1+tlrc[r1#0_Coef] could not be loaded
** ERROR: Dset DBD_A25_r2+tlrc[r2#0_Coef] could not be loaded
** ERROR: Dset DBD_A26_r1+tlrc[r1#0_Coef] could not be loaded
** ERROR: Dset DBD_A26_r2+tlrc[r2#0_Coef] could not be loaded
** ERROR: Dset DBD_A27_r1+tlrc[r1#0_Coef] could not be loaded
** ERROR: Dset DBD_A27_r2+tlrc[r2#0_Coef] could not be loaded
** ERROR: Dset DBD_A28_r1+tlrc[r1#0_Coef] could not be loaded
** ERROR: Dset DBD_A28_r2+tlrc[r2#0_Coef] could not be loaded
** ERROR: Dset DBD_A01_r1+tlrc[r1#0_Coef] could not be loaded
** ERROR: Dset DBD_A01_r2+tlrc[r2#0_Coef] could not be loaded
** ERROR: Dset DBD_A02_r1+tlrc[r1#0_Coef] could not be loaded
** ERROR: Dset DBD_A02_r2+tlrc[r2#0_Coef] could not be loaded
** ERROR: Dset DBD_A04_r1+tlrc[r1#0_Coef] could not be loaded
** ERROR: Dset DBD_A04_r2+tlrc[r2#0_Coef] could not be loaded
** ERROR: Dset DBD_A09_r1+tlrc[r1#0_Coef] could not be loaded
** ERROR: Dset DBD_A09_r2+tlrc[r2#0_Coef] could not be loaded
** ERROR: Dset DBD_A12_r1+tlrc[r1#0_Coef] could not be loaded
** ERROR: Dset DBD_A12_r2+tlrc[r2#0_Coef] could not be loaded
** ERROR: Dset DBD_A14_r1+tlrc[r1#0_Coef] could not be loaded
** ERROR: Dset DBD_A14_r2+tlrc[r2#0_Coef] could not be loaded
** ERROR: Dset DBD_A16_r1+tlrc[r1#0_Coef] could not be loaded
** ERROR: Dset DBD_A16_r2+tlrc[r2#0_Coef] could not be loaded
** ERROR: Dset DBD_A17_r1+tlrc[r1#0_Coef] could not be loaded
** ERROR: Dset DBD_A17_r2+tlrc[r2#0_Coef] could not be loaded
** ERROR: Dset DBD_A18_r1+tlrc[r1#0_Coef] could not be loaded
** ERROR: Dset DBD_A18_r2+tlrc[r2#0_Coef] could not be loaded
** ERROR: Dset DBD_A19_r1+tlrc[r1#0_Coef] could not be loaded
** ERROR: Dset DBD_A19_r2+tlrc[r2#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 · May 26, 2017, 7:30pm

Sophia,

OK, that error message gives a better understanding about the problem. Basically, the issue is that those input files could not be found. Make sure those files are under the current directory where you ran the 3dLME script. If not, you would have to provide the path as part of the input files.

sophia · May 26, 2017, 9:11pm

Hi Gang, the input files were under the current directory where I ran the 3dLME script/text. So, just in case, I removed ‘[r*#0_Coef]’ from each line in the script/text (-dataTable), and ran the script/text again. It is now working (giving some logs, such as "Z slice * done: 05/26/17 17:03:23.924 ").

Subj cond group InputFile
DBD_A00 r1 ag DBD_A00_r1+tlrc ‘[r1#0_Coef]’ \

I thought that this ‘[r1#0_Coef]’ needed to be included for each line (=dataTable) in the script (I followed the example provided by the AFNI website), but things are now working without it included. I will wait for the results to come up, but if running the text in this way is incorrect, please let me know.

Thanks again for your quick responses.
Sophia