3dANOVA command line error

AFNI Message Board
1

Thanks in advance for your help with this issue.

I am attempting to run 3dANOVA for comparing a single measure across 3 groups (grp1, grp2, grp3) but I encounter the following error. Any suggestions on how to fix the issue?

**Error: Unrecognized command line option: 1
Here’s hoping these excerpts from ‘3dANOVA -help’ enlighten:
‘(1) Faces, (2) Houses, and (3) Donuts’
‘-dset 1 filename : data set for factor level 1’
‘-dset 1 filename data set for factor level 1’

My script is set as up recommended by 3dANOVA -help:

#!/bin/tcsh
3dANOVA -levels 3
-dset 1 path_to_file/input_file
-dset 1 …
-dset 1 …
-dset 2 path_to_file/input_file
-dset 2 …
-dset 2 …
-dset 3 path_to_file/input_file
-dset 3 …
-dset 3 …
-mask path to file/mask
-ftr group
-mean 1 grp1
-mean 2 grp2
-mean 3 grp3
-diff grp1vsgrp2
-diff grp2vsgrp3
-diff grp1vsgrp3
-contr 1 1 -1 grp1grp2vsgrp3
-contr -1 1 1 grp1vsgrp2grp3
-contr 1 -1 1 grp1grp3vsgrp2
-bucket prefix

2

Feel free to post your entire command in a code box. But likely caused by not having a backslash continuation at the end of each filename. In linux/unix a "" will tell the shell to continue to the next line and keep reading inputs. So each line in the command should end with that except the last one.

3

Hi Peter,

Thanks for your feedback. I did have a "" following the last line. I removed it but that did not resolve the issue. Same error.

4

Hi Jesse,

Peter had a good suggestion to post the entire command. If you are uncomfortable doing that, please feel free to mail me the script file (click on my name for the address).

  • rick
5

Thanks for the script. The -diff options are missing indices. I will try to clarify that failure.

Note that there is gen_group_command.py to help write such commands (though it does not really help with -diff and -contr, say).

  • rick
6

Thanks Rick. Adding indices to the -diff argument fixed the issue.