3dLME "no traceback available"

ndalbert · April 11, 2018, 1:18pm

Hi AFNI experts (most directly, Gang),

I am trying to run a 3dLME command and am having some troubles with what appears to be the reading of the input files.

I am trying to measure the difference in the correlation between my I.V. (SSRT) and BOLD activity between two different time points. Time point 1 = BL, Time point 2 = FU2. The model pasted below is what I am using to run this. What I think I have set up is: GLT1 = the effect of SSRT on BOLD at BL; GLT2 = the effect of SSRT on BOLD at FU2; GLT3 = the difference between the effect of SSRT at BL and the effect of SSRT at FU2. Here are a few details that might be helpful:

there are 538 total participants (only 5 shown here for brevity). All participants have data for both BL and FU2 time pints. In my dataTable, the last line of the table does not include a .
The input files that I am calling on are separate contrasts for stop-related activity generated from the first level GLM. Therefore, there are no sub-briks. The file contains only 1 data point per voxel.
I tried running the same model using 3dMVM (because I have equal number of subjects), but the results were completely null (either “N/A” or “0.00” throughout the results table).
I have run this same command with and without the ’ surrounding the filenames, and it does not make a difference.
the file paths are correct

Here is the command I am using:

3dLME -prefix SSRT -jobs 1
-mask StdGMmask_resampled+tlrc.HEAD
-model ‘SSRTTime’
-qVars ‘SSRT’
-qVarCenters ‘215’
-ranEff ‘~1+SSRT’
-SS_type 3
-num_glt 3
-gltLabel 1 ‘BL_Effects’ -gltCode 1 'Time : 1BL SSRT :’
-gltLabel 2 ‘FU2_Effects’ -gltCode 2 ‘Time : 1FU2 SSRT :’
-gltLabel 3 ‘BL_v_FU2’ -gltCode 3 'Time : -1BL 1*FU2 SSRT :’
-dataTable
Subjects Time SSRT InputFile
s01 BL 255.5 ‘/Volumes/NickBackUp/StopConRegressions/LME/BL_538/000000240546_BL_stopcon.nii’
s01 FU2 257 ‘/Volumes/NickBackUp/StopConRegressions/LME/FU2_538/000000240546_FU2_stopcon.nii’
s02 BL 202.46 ‘/Volumes/NickBackUp/StopConRegressions/LME/BL_538/000000297685_BL_stopcon.nii’
s02 FU2 206 ‘/Volumes/NickBackUp/StopConRegressions/LME/FU2_538/000000297685_FU2_stopcon.nii’
s03 BL 275 ‘/Volumes/NickBackUp/StopConRegressions/LME/BL_538/000000469693_BL_stopcon.nii’
s03 FU2 175 ‘/Volumes/NickBackUp/StopConRegressions/LME/FU2_538/000000469693_FU2_stopcon.nii’
s04 BL 246.83 ‘/Volumes/NickBackUp/StopConRegressions/LME/BL_538/000000556983_BL_stopcon.nii’
s04 FU2 223 ‘/Volumes/NickBackUp/StopConRegressions/LME/FU2_538/000000556983_FU2_stopcon.nii’
s05 BL 272.25 ‘/Volumes/NickBackUp/StopConRegressions/LME/BL_538/000000613223_BL_stopcon.nii’
s05 FU2 244 ‘/Volumes/NickBackUp/StopConRegressions/LME/FU2_538/000000613223_FU2_stopcon.nii’
…

when I run this, I get the following output:

Loading required package: nlme
Package nlme loaded successfully!

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

Warning messages:
1: package ‘car’ was built under R version 3.4.4
2: package ‘carData’ was built under R version 3.4.4

++++++++++++++++++++++++++++++++++++++++++++++++++++
***** Summary information of data structure *****
#####this goes on to list the summary of the subjects and data…

Contingency tables of subject distributions among the categorical variables:

Tabulation of subjects against all categorical variables

Subj vs Time:
      
       BL FU2
  s01   1   1
  s02   1   1
  s03   1   1
  s04   1   1
  s05   1   1
... ######  this goes on throughout all 538 participants....


###### AND THEN THIS ERROR:
No traceback available 
e[7m** ERROR:e[0m Dset s01 could not be loaded
Warning in parse.AFNI.name(filename) :
  filename >>s01<< not a character string

###### for each participant...
######and this at the very end:

** 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.

###### when I run this 3difo command, all the data is exactly the same. 


Please let me know where you think the error is coming from and what I should do to address this.

Thank you for the help, 

Nick

Gang · April 11, 2018, 9:46pm

Nick:

The problem is this part:

e[7m** ERROR:e[0m Dset s01 could not be loaded

One possibility is that you have an incorrect input filename or some bad character embedded in the filename. If you cannot identify it, try running the following command:

file_tool -test -infiles my_script.txt

ndalbert · April 12, 2018, 1:25pm

Hi Gang, thanks for responding.

when I run file_tool -test -infiles my_script.txt on my script, I get the following:

file ‘x.3dLME’: missing final newline
x.3dLME has 0 bad characters

x.3dLME file type: UNIX

I am not sure what the means.

Thank you
Nick

Gang · April 12, 2018, 3:15pm

file ‘x.3dLME’: missing final newline

Add a new (and empty) line at the end of the script, and see if that fixes the problem. If the problem persists, send me a copy of the script.

ndalbert · April 12, 2018, 6:04pm

Hi Gang,

the problem is persisting and I have emailed you a copy of the script with the email subject: 3dLME “no traceback available”

Thank you
Nick