Hello,
I am trying to run an ANOVA on a group of participants with the following script:
3dANOVA2 -type 3 -alevels 6 -blevels 18 \
-dset 1 1 DN101+tlrc \
-dset 2 1 DW101+tlrc \
-dset 3 1 DL101+tlrc \
-dset 4 1 LN101+tlrc \
-dset 5 1 LW101+tlrc \
-dset 6 1 WN101+tlrc \
-dset 1 3 DN3+tlrc \
-dset 2 3 DW3+tlrc \
-dset 3 3 DL3+tlrc \
-dset 4 3 LN3+tlrc \
-dset 5 3 LW3+tlrc \
-dset 6 3 WN3+tlrc \
-dset 1 4 DN4+tlrc \
-dset 2 4 DW4+tlrc \
-dset 3 4 DL4+tlrc \
-dset 4 4 LN4+tlrc \
-dset 5 4 LW4+tlrc \
-dset 6 4 WN4+tlrc \
-dset 1 5 DN5+tlrc \
-dset 2 5 DW5+tlrc \
-dset 3 5 DL5+tlrc \
-dset 4 5 LN5+tlrc \
-dset 5 5 LW5+tlrc \
-dset 6 5 WN5+tlrc \
-dset 1 6 DN6+tlrc \
-dset 2 6 DW6+tlrc \
-dset 3 6 DL6+tlrc \
-dset 4 6 LN6+tlrc \
-dset 5 6 LW6+tlrc \
-dset 6 6 WN6+tlrc \
-dset 1 7 DN7+tlrc \
-dset 2 7 DW7+tlrc \
-dset 3 7 DL7+tlrc \
-dset 4 7 LN7+tlrc \
-dset 5 7 LW7+tlrc \
-dset 6 7 WN7+tlrc \
-dset 1 8 DN8+tlrc \
-dset 2 8 DW8+tlrc \
-dset 3 8 DL8+tlrc \
-dset 4 8 LN8+tlrc \
-dset 5 8 LW8+tlrc \
-dset 6 8 WN8+tlrc \
-dset 1 9 DN9+tlrc \
-dset 2 9 DW9+tlrc \
-dset 3 9 DL9+tlrc \
-dset 4 9 LN9+tlrc \
-dset 5 9 LW9+tlrc \
-dset 6 9 WN9+tlrc \
-dset 1 10 DN10+tlrc \
-dset 2 10 DW10+tlrc \
-dset 3 10 DL10+tlrc \
-dset 4 10 LN10+tlrc \
-dset 5 10 LW10+tlrc \
-dset 6 10 WN10+tlrc \
-dset 1 11 DN11+tlrc \
-dset 2 11 DW11+tlrc \
-dset 3 11 DL11+tlrc \
-dset 4 11 LN11+tlrc \
-dset 5 11 LW11+tlrc \
-dset 6 11 WN11+tlrc \
-dset 1 14 DN14+tlrc \
-dset 2 14 DW14+tlrc \
-dset 3 14 DL14+tlrc \
-dset 4 14 LN14+tlrc \
-dset 5 14 LW14+tlrc \
-dset 6 14 WN14+tlrc \
-dset 1 15 DN15+tlrc \
-dset 2 15 DW15+tlrc \
-dset 3 15 DL15+tlrc \
-dset 4 15 LN15+tlrc \
-dset 5 15 LW15+tlrc \
-dset 6 15 WN15+tlrc \
-dset 1 16 DN16+tlrc \
-dset 2 16 DW16+tlrc \
-dset 3 16 DL16+tlrc \
-dset 4 16 LN16+tlrc \
-dset 5 16 LW16+tlrc \
-dset 6 16 WN16+tlrc \
-dset 1 17 DN17+tlrc \
-dset 2 17 DW17+tlrc \
-dset 3 17 DL17+tlrc \
-dset 4 17 LN17+tlrc \
-dset 5 17 LW17+tlrc \
-dset 6 17 WN17+tlrc \
-dset 1 18 DN18+tlrc \
-dset 2 18 DW18+tlrc \
-dset 3 18 DL18+tlrc \
-dset 4 18 LN18+tlrc \
-dset 5 18 LW18+tlrc \
-dset 6 18 WN18+tlrc \
-dset 1 19 DN19+tlrc \
-dset 2 19 DW19+tlrc \
-dset 3 19 DL19+tlrc \
-dset 4 19 LN19+tlrc \
-dset 5 19 LW19+tlrc \
-dset 6 19 WN19+tlrc \
-dset 1 20 DN20+tlrc \
-dset 2 20 DW20+tlrc \
-dset 3 20 DL20+tlrc \
-dset 4 20 LN20+tlrc \
-dset 5 20 LW20+tlrc \
-dset 6 20 WN20+tlrc \
-dset 1 21 DN21+tlrc \
-dset 2 21 DW21+tlrc \
-dset 3 21 DL21+tlrc \
-dset 4 21 LN21+tlrc \
-dset 5 21 LW21+tlrc \
-dset 6 21 WN21+tlrc \
-fa FtestlevelA \
-amean 1 DW \
-amean 2 DL \
-amean 3 DN \
-amean 4 LW \
-amean 5 LN \
-amean 6 WN \
-adiff 1 2 DW_DN \
-adiff 1 3 DL_DN \
-adiff 4 5 LW_LN \
-adiff 3 5 DN_LN \
-adiff 3 6 DN_WN \
-adiff 4 6 LN_WN \
-bucket grp2anova_blk_evt
But I get the following error:
** FATAL ERROR: Program 3dANOVA2: illegal argument after -dset
Any advice would be really appreciated
Thank you!
rickr
January 12, 2020, 5:58pm
2
Hi Nicole,
Might that be just because you need -blevels 21? I will check better when I am at my computer…
Hi Rick,
I have only 18 participants, as 3 had to be removed.
Is my formatting for the arguments possibly incorrect?
Thank you,
Hello,
As an update, I fixed the spacing of the backward slash, and that seemed to help, but I am getting a new issue. I get the following output:
** ERROR: Unrecognized command line option: 1
Here's hoping these excerpts from '3dANOVA2 -help' enlighten:
'(1) chocolate, (2) glazed, (3) sugar'
'(1) fred, (2) ethel, (3) lucy, (4) ricky'
'-dset 1 1 filename : data set for level 1 of factor A'
TO note, although I have ensured that I have every relevant file in the folder, a few of the individual dsets get the following message:
> -dset 4 5 LN5+tlrc
Display all 217 possibilities? (y or n)
DL10+tlrc.BRIK DN10+tlrc.HEAD
....
DL14+tlrc.HEAD DN15+tlrc.BRIK
Which makes me believe that possibly there is an issue in finding the files or something is wrong with my syntax?
Thanks!
rickr
January 18, 2020, 9:13pm
5
Hi Nicole,
Can you give the updated command to check?
Also, run the script through file_tool, to see if it has any suggestions, e.g.,
file_tool -test -infile MYSCRIPT.txt
Hi Rick,
Attached is the formatted script:
3dANOVA2 -type 3 -alevels 6 -blevels 18 \
-dset 1 1 DN101+tlrc \
-dset 2 1 DW101+tlrc \
-dset 3 1 DL101+tlrc \
-dset 4 1 LN101+tlrc \
-dset 5 1 LW101+tlrc \
-dset 6 1 WN101+tlrc \
-dset 1 3 DN3+tlrc \
-dset 2 3 DW3+tlrc \
-dset 3 3 DL3+tlrc \
-dset 4 3 LN3+tlrc \
-dset 5 3 LW3+tlrc \
-dset 6 3 WN3+tlrc \
-dset 1 4 DN4+tlrc \
-dset 2 4 DW4+tlrc \
-dset 3 4 DL4+tlrc \
-dset 4 4 LN4+tlrc \
-dset 5 4 LW4+tlrc \
-dset 6 4 WN4+tlrc \
-dset 1 5 DN5+tlrc \
-dset 2 5 DW5+tlrc \
-dset 3 5 DL5+tlrc \
-dset 4 5 LN5+tlrc \
-dset 5 5 LW5+tlrc \
-dset 6 5 WN5+tlrc \
-dset 1 6 DN6+tlrc \
-dset 2 6 DW6+tlrc \
-dset 3 6 DL6+tlrc \
-dset 4 6 LN6+tlrc \
-dset 5 6 LW6+tlrc \
-dset 6 6 WN6+tlrc \
-dset 1 7 DN7+tlrc \
-dset 2 7 DW7+tlrc \
-dset 3 7 DL7+tlrc \
-dset 4 7 LN7+tlrc \
-dset 5 7 LW7+tlrc \
-dset 6 7 WN7+tlrc \
-dset 1 8 DN8+tlrc \
-dset 2 8 DW8+tlrc \
-dset 3 8 DL8+tlrc \
-dset 4 8 LN8+tlrc \
-dset 5 8 LW8+tlrc \
-dset 6 8 WN8+tlrc \
-dset 1 9 DN9+tlrc \
-dset 2 9 DW9+tlrc \
-dset 3 9 DL9+tlrc \
-dset 4 9 LN9+tlrc \
-dset 5 9 LW9+tlrc \
-dset 6 9 WN9+tlrc \
-dset 1 10 DN10+tlrc \
-dset 2 10 DW10+tlrc \
-dset 3 10 DL10+tlrc \
-dset 4 10 LN10+tlrc \
-dset 5 10 LW10+tlrc \
-dset 6 10 WN10+tlrc \
-dset 1 11 DN11+tlrc \
-dset 2 11 DW11+tlrc \
-dset 3 11 DL11+tlrc \
-dset 4 11 LN11+tlrc \
-dset 5 11 LW11+tlrc \
-dset 6 11 WN11+tlrc \
-dset 1 14 DN14+tlrc \
-dset 2 14 DW14+tlrc \
-dset 3 14 DL14+tlrc \
-dset 4 14 LN14+tlrc \
-dset 5 14 LW14+tlrc \
-dset 6 14 WN14+tlrc \
-dset 1 15 DN15+tlrc \
-dset 2 15 DW15+tlrc \
-dset 3 15 DL15+tlrc \
-dset 4 15 LN15+tlrc \
-dset 5 15 LW15+tlrc \
-dset 6 15 WN15+tlrc \
-dset 1 16 DN16+tlrc \
-dset 2 16 DW16+tlrc \
-dset 3 16 DL16+tlrc \
-dset 4 16 LN16+tlrc \
-dset 5 16 LW16+tlrc \
-dset 6 16 WN16+tlrc \
-dset 1 17 DN17+tlrc \
-dset 2 17 DW17+tlrc \
-dset 3 17 DL17+tlrc \
-dset 4 17 LN17+tlrc \
-dset 5 17 LW17+tlrc \
-dset 6 17 WN17+tlrc \
-dset 1 18 DN18+tlrc \
-dset 2 18 DW18+tlrc \
-dset 3 18 DL18+tlrc \
-dset 4 18 LN18+tlrc \
-dset 5 18 LW18+tlrc \
-dset 6 18 WN18+tlrc \
-dset 1 19 DN19+tlrc \
-dset 2 19 DW19+tlrc \
-dset 3 19 DL19+tlrc \
-dset 4 19 LN19+tlrc \
-dset 5 19 LW19+tlrc \
-dset 6 19 WN19+tlrc \
-dset 1 20 DN20+tlrc \
-dset 2 20 DW20+tlrc \
-dset 3 20 DL20+tlrc \
-dset 4 20 LN20+tlrc \
-dset 5 20 LW20+tlrc \
-dset 6 20 WN20+tlrc \
-dset 1 21 DN21+tlrc \
-dset 2 21 DW21+tlrc \
-dset 3 21 DL21+tlrc \
-dset 4 21 LN21+tlrc \
-dset 5 21 LW21+tlrc \
-dset 6 21 WN21+tlrc \
-amean 1 DW \
-amean 2 DL \
-amean 3 DN \
-amean 4 LW \
-amean 5 LN \
-amean 6 WN \
-adiff 1 2 DW_DN \
-adiff 1 3 DL_DN \
-adiff 4 5 LW_LN \
-adiff 3 5 DN_LN \
-adiff 3 6 DN_WN \
-adiff 4 6 LN_WN \
-fa FtestlevelA \
-bucket grp2anova_blk_evt
For some reason, running through file_tool is not working- I’m not familiar with this command, so I may be using it incorrectly. (I am getting this following message
Thank you
rickr
January 21, 2020, 7:32pm
7
I think you still need to adjust it to have -blevels 21. Please fix that on the first line of the script. It might be the reason for the error message, which could be more clear (I have made a change for that).
Regarding file_tool, I suspect you are just not giving it the correct path to the script. Make sure “ls” works, first. But at least with what I can copy from here, file_tool does not suggest any problems, so it might just be -blevels.
Hi Rick,
After adjusting -blevels 21, I am getting the same error, even if I run through file_path. This is the error:
** ERROR: Unrecognized command line option: 1
Here's hoping these excerpts from '3dANOVA2 -help' enlighten:
'(1) chocolate, (2) glazed, (3) sugar'
'(1) fred, (2) ethel, (3) lucy, (4) ricky'
'-dset 1 1 filename : data set for level 1 of factor A'
Thanks!
As well, when I run file_tool, I get a message saying that it has “0 bad characters”
Thanks
rickr
January 24, 2020, 8:46pm
10
I did not realize that you actually had missing data here. So -blevels 18 was correct, but then all of the -dsets options had to be fixed.
If the datasets were named more like: SUBJ_LABEL, e.g. s07_DL+tlrc, then it would be very easy to use gen_group_command.py to quickly write this script. Putting the subject ID first would allow file sorting to be in subject-major order, rather than subject-minor order.
Anyway, once I adjusted the b-indexing, the command ran.
nstuart
January 31, 2020, 4:37pm
11
Hi Rick,
Thank you for this. I fixed the b-indexing, as well as changing the file names. However, if I run this script:
3dANOVA2 -type 3 -alevels 6 -blevels 18 \
-dset 1 1 p101_DN+tlrc \
-dset 2 1 p101_DW+tlrc \
-dset 3 1 p101_DL+tlrc \
-dset 4 1 p101_LN+tlrc \
-dset 5 1 p101_LW+tlrc \
-dset 6 1 p101_WN+tlrc \
-dset 1 2 p03_DN+tlrc \
-dset 2 2 p03_DW+tlrc \
-dset 3 2 p03_DL+tlrc \
-dset 4 2 p03_LN+tlrc \
-dset 5 2 p03_LW+tlrc \
-dset 6 2 p03_WN+tlrc \
-dset 1 3 p04_DN+tlrc \
-dset 2 3 p04_DW+tlrc \
-dset 3 3 p04_DL+tlrc \
-dset 4 3 p04_LN+tlrc \
-dset 5 3 p04_LW+tlrc \
-dset 6 3 p04_WN+tlrc \
-dset 1 4 p05_DN+tlrc \
-dset 2 4 p05_DW+tlrc \
-dset 3 4 p05_DL+tlrc \
-dset 4 4 p05_LN+tlrc \
-dset 5 4 p05_LW+tlrc \
-dset 6 4 p05_WN+tlrc \
-dset 1 5 p06_DN+tlrc \
-dset 2 5 p06_DW+tlrc \
-dset 3 5 p06_DL+tlrc \
-dset 4 5 p06_LN+tlrc \
-dset 5 5 p06_LW+tlrc \
-dset 6 5 p06_WN+tlrc \
-dset 1 6 p07_DN+tlrc \
-dset 2 6 p07_DW+tlrc \
-dset 3 6 p07_DL+tlrc \
-dset 4 6 p07_LN+tlrc \
-dset 5 6 p07_LW+tlrc \
-dset 6 6 p07_WN+tlrc \
-dset 1 7 p08_DN+tlrc \
-dset 2 7 p08_DW+tlrc \
-dset 3 7 p08_DL+tlrc \
-dset 4 7 p08_LN+tlrc \
-dset 5 7 p08_LW+tlrc \
-dset 6 7 p08_WN+tlrc \
-dset 1 8 p09_DN+tlrc \
-dset 2 8 p09_DW+tlrc \
-dset 3 8 p09_DL+tlrc \
-dset 4 8 p09_LN+tlrc \
-dset 5 8 p09_LW+tlrc \
-dset 6 8 p09_WN+tlrc \
-dset 1 9 p10_DN+tlrc \
-dset 2 9 p10_DW+tlrc \
-dset 3 9 p10_DL+tlrc \
-dset 4 9 p10_LN+tlrc \
-dset 5 9 p10_LW+tlrc \
-dset 6 9 p10_WN+tlrc \
-dset 1 10 p11_DN+tlrc \
-dset 2 10 p11_DW+tlrc \
-dset 3 10 p11_DL+tlrc \
-dset 4 10 p11_LN+tlrc \
-dset 5 10 p11_LW+tlrc \
-dset 6 10 p11_WN+tlrc \
-dset 1 11 p14_DN+tlrc \
-dset 2 11 p14_DW+tlrc \
-dset 3 11 p14_DL+tlrc \
-dset 4 11 p14_LN+tlrc \
-dset 5 11 p14_LW+tlrc \
-dset 6 11 p14_WN+tlrc \
-dset 1 12 p15_DN+tlrc \
-dset 2 12 p15_DW+tlrc \
-dset 3 12 p15_DL+tlrc \
-dset 4 12 p15_LN+tlrc \
-dset 5 12 p15_LW+tlrc \
-dset 6 12 p15_WN+tlrc \
-dset 1 13 p16_DN+tlrc \
-dset 2 13 p16_DW+tlrc \
-dset 3 13 p16_DL+tlrc \
-dset 4 13 p16_LN+tlrc \
-dset 5 13 p16_LW+tlrc \
-dset 6 13 p16_WN+tlrc \
-dset 1 14 p17_DN+tlrc \
-dset 2 14 p17_DW+tlrc \
-dset 3 14 p17_DL+tlrc \
-dset 4 14 p17_LN+tlrc \
-dset 5 14 p17_LW+tlrc \
-dset 6 14 p17_WN+tlrc \
-dset 1 15 p18_DN+tlrc \
-dset 2 15 p18_DW+tlrc \
-dset 3 15 p18_DL+tlrc \
-dset 4 15 p18_LN+tlrc \
-dset 5 15 p18_LW+tlrc \
-dset 6 15 p18_WN+tlrc \
-dset 1 16 p19_DN+tlrc \
-dset 2 16 p19_DW+tlrc \
-dset 3 16 p19_DL+tlrc \
-dset 4 16 p19_LN+tlrc \
-dset 5 16 p19_LW+tlrc \
-dset 6 16 p19_WN+tlrc \
-dset 1 17 p20_DN+tlrc \
-dset 2 17 p20_DW+tlrc \
-dset 3 17 p20_DL+tlrc \
-dset 4 17 p20_LN+tlrc \
-dset 5 17 p20_LW+tlrc \
-dset 6 17 p20_WN+tlrc \
-dset 1 18 p21_DN+tlrc \
-dset 2 18 p21_DW+tlrc \
-dset 3 18 p21_DL+tlrc \
-dset 4 18 p21_LN+tlrc \
-dset 5 18 p21_LW+tlrc \
-dset 6 18 p21_WN+tlrc \
-amean 1 DW \
-amean 2 DL \
-amean 3 DN \
-amean 4 LW \
-amean 5 LN \
-amean 6 WN \
-adiff 1 2 DW_DN \
-adiff 1 3 DL_DN \
-adiff 4 5 LW_LN \
-adiff 3 5 DN_LN \
-adiff 3 6 DN_WN \
-adiff 4 6 LN_WN \
-fa FtestlevelA \
-bucket grp2anova_blk_evt
I still get the following error:
I’m having trouble figuring out using gen_group_command.py, because there are 6 levels for each participant. Do you have any advice for trying this method?
Thank you so much.
rickr
January 31, 2020, 11:44pm
12
Hi Nicole,
Sorry this is so much trouble. This command is more readable with the file names. In fact, I can run your exact command without any errors (using local files that match yours). Is there anything else to the script? Is this the exact command in your script?
Regarding ggc.py, I did not think it through. That tool is set up to take inputs where all sub-bricks for one subject are in a single dataset. So it might be easiest to start with the more original datasets. But just to demonstrate, consider this tcsh script to first copy the data to a new directory and new files, then run gen_group_command.py on it.
# -------------------------------------------------------
# make bucket datasets in a new directory
set newdir = data.buckets
mkdir $newdir
set slist = ( `\ls -1 p[0-9]*+tlrc.HEAD | awk -F_ '{print $1}' | sort | uniq` )
set ltext = 'DN,DW,DL,LN,LW,WN'
foreach sid ( $slist )
3dbucket -prefix $newdir/${sid}_all ${sid}_{$ltext}+tlrc.HEAD
end
cd $newdir
# -------------------------------------------------------
# create a 3dANOVA2 command script
gen_group_command.py -command 3dANOVA2 \
-write_script cmd.3dANOVA2 \
-dsets *.HEAD -subs_betas 0 1 2 3 4 5
You can use -options to add on to that in the ggc.py command, or you can just edit the script to add -adiff and related options.
Note that in your command, the order of the datasets does not quite match the order applied in -amean and -adiff options. The files come as DN DW DL LN LW WN, so some of those need adjusting.
Does that sound easier? At least it would give you a script to start with. You can use labels for -subs_betas, to use something more clear than 0 1 2 3 4 5.
nstuart
February 7, 2020, 3:57pm
13
Hi Rick,
I’ve adjusted the -amean and -adiff options. My exact script is pasted here again
3dANOVA2 -type 3 -alevels 6 -blevels 18 \
-dset 1 1 p101_DN+tlrc \
-dset 2 1 p101_DW+tlrc \
-dset 3 1 p101_DL+tlrc \
-dset 4 1 p101_LN+tlrc \
-dset 5 1 p101_LW+tlrc \
-dset 6 1 p101_WN+tlrc \
-dset 1 2 p03_DN+tlrc \
-dset 2 2 p03_DW+tlrc \
-dset 3 2 p03_DL+tlrc \
-dset 4 2 p03_LN+tlrc \
-dset 5 2 p03_LW+tlrc \
-dset 6 2 p03_WN+tlrc \
-dset 1 3 p04_DN+tlrc \
-dset 2 3 p04_DW+tlrc \
-dset 3 3 p04_DL+tlrc \
-dset 4 3 p04_LN+tlrc \
-dset 5 3 p04_LW+tlrc \
-dset 6 3 p04_WN+tlrc \
-dset 1 4 p05_DN+tlrc \
-dset 2 4 p05_DW+tlrc \
-dset 3 4 p05_DL+tlrc \
-dset 4 4 p05_LN+tlrc \
-dset 5 4 p05_LW+tlrc \
-dset 6 4 p05_WN+tlrc \
-dset 1 5 p06_DN+tlrc \
-dset 2 5 p06_DW+tlrc \
-dset 3 5 p06_DL+tlrc \
-dset 4 5 p06_LN+tlrc \
-dset 5 5 p06_LW+tlrc \
-dset 6 5 p06_WN+tlrc \
-dset 1 6 p07_DN+tlrc \
-dset 2 6 p07_DW+tlrc \
-dset 3 6 p07_DL+tlrc \
-dset 4 6 p07_LN+tlrc \
-dset 5 6 p07_LW+tlrc \
-dset 6 6 p07_WN+tlrc \
-dset 1 7 p08_DN+tlrc \
-dset 2 7 p08_DW+tlrc \
-dset 3 7 p08_DL+tlrc \
-dset 4 7 p08_LN+tlrc \
-dset 5 7 p08_LW+tlrc \
-dset 6 7 p08_WN+tlrc \
-dset 1 8 p09_DN+tlrc \
-dset 2 8 p09_DW+tlrc \
-dset 3 8 p09_DL+tlrc \
-dset 4 8 p09_LN+tlrc \
-dset 5 8 p09_LW+tlrc \
-dset 6 8 p09_WN+tlrc \
-dset 1 9 p10_DN+tlrc \
-dset 2 9 p10_DW+tlrc \
-dset 3 9 p10_DL+tlrc \
-dset 4 9 p10_LN+tlrc \
-dset 5 9 p10_LW+tlrc \
-dset 6 9 p10_WN+tlrc \
-dset 1 10 p11_DN+tlrc \
-dset 2 10 p11_DW+tlrc \
-dset 3 10 p11_DL+tlrc \
-dset 4 10 p11_LN+tlrc \
-dset 5 10 p11_LW+tlrc \
-dset 6 10 p11_WN+tlrc \
-dset 1 11 p14_DN+tlrc \
-dset 2 11 p14_DW+tlrc \
-dset 3 11 p14_DL+tlrc \
-dset 4 11 p14_LN+tlrc \
-dset 5 11 p14_LW+tlrc \
-dset 6 11 p14_WN+tlrc \
-dset 1 12 p15_DN+tlrc \
-dset 2 12 p15_DW+tlrc \
-dset 3 12 p15_DL+tlrc \
-dset 4 12 p15_LN+tlrc \
-dset 5 12 p15_LW+tlrc \
-dset 6 12 p15_WN+tlrc \
-dset 1 13 p16_DN+tlrc \
-dset 2 13 p16_DW+tlrc \
-dset 3 13 p16_DL+tlrc \
-dset 4 13 p16_LN+tlrc \
-dset 5 13 p16_LW+tlrc \
-dset 6 13 p16_WN+tlrc \
-dset 1 14 p17_DN+tlrc \
-dset 2 14 p17_DW+tlrc \
-dset 3 14 p17_DL+tlrc \
-dset 4 14 p17_LN+tlrc \
-dset 5 14 p17_LW+tlrc \
-dset 6 14 p17_WN+tlrc \
-dset 1 15 p18_DN+tlrc \
-dset 2 15 p18_DW+tlrc \
-dset 3 15 p18_DL+tlrc \
-dset 4 15 p18_LN+tlrc \
-dset 5 15 p18_LW+tlrc \
-dset 6 15 p18_WN+tlrc \
-dset 1 16 p19_DN+tlrc \
-dset 2 16 p19_DW+tlrc \
-dset 3 16 p19_DL+tlrc \
-dset 4 16 p19_LN+tlrc \
-dset 5 16 p19_LW+tlrc \
-dset 6 16 p19_WN+tlrc \
-dset 1 17 p20_DN+tlrc \
-dset 2 17 p20_DW+tlrc \
-dset 3 17 p20_DL+tlrc \
-dset 4 17 p20_LN+tlrc \
-dset 5 17 p20_LW+tlrc \
-dset 6 17 p20_WN+tlrc \
-dset 1 18 p21_DN+tlrc \
-dset 2 18 p21_DW+tlrc \
-dset 3 18 p21_DL+tlrc \
-dset 4 18 p21_LN+tlrc \
-dset 5 18 p21_LW+tlrc \
-dset 6 18 p21_WN+tlrc \
-amean 1 DN \
-amean 2 DW \
-amean 3 DL \
-amean 4 LN \
-amean 5 LW \
-amean 6 WN \
-adiff 1 3 DN_DL \
-adiff 1 2 DN_DW \
-adiff 4 5 LN_LW \
-adiff 1 4 DN_LN \
-adiff 1 6 DN_WN \
-adiff 4 6 LN_WN \
-fa FtestlevelA \
-bucket grp2anova_blk_evt
I really have no idea why I am continuing to get the following error:
I’ve triple checked to make sure that every relevant file is in the directory. I have both the HEAD and BRIK files for each of these levels and participants (i.e. there is p101_DN+tlrc.HEAD and p101_DN+tlrc.BRIK in the directory). Do I need both of these types of files, or only the HEAD files? If only one type is needed, maybe that is a problem?
Thank you,
nstuart
February 7, 2020, 4:02pm
14
AS well, while running it I am noticing that for pretty much each line, I get the following message as it runs:
-dset 1 1 p101_DN+tlrc.HEAD 1 p101_DW+tlrc.HEAD
Does this possibly indicate that something is going wrong in actually using the files?
Thanks,
rickr
February 7, 2020, 5:36pm
15
Hi Nicole,
Ooooh, the “Display all 110 possibilities” is very helpful…
For the record, I can run your script successfully as is. And I can reproduce the error if I paste it into a bash terminal window.
Maybe you are running bash, and maybe you are using copy-and-paste to run the script. In that case, the TAB characters work to prompt to “Display all 110 possibilities” for file completion.
Since the script has no spaces toward the ends of the lines (it has only tabs (e.g. after 18 and all of the +tlrc’s)), and since there are no spaces at the beginnings of the lines, those tabs disappear and the end of one line connects to the beginning of the next.
To be specific, the first “18” (for -blevels) is connecting to the subsequent “-dset”, making the next option to be seen a “1”, and without any -dset option.
Anyway, put this script in a file and run it via either tcsh or bash (either should be okay as it is written), e.g.
tcsh -x my.anova.script
One general rule that will help readability and avoid these issues: indent any continued lines. That is to say, add some spaces before all of the -dset and following options.
Anyway, let me know if that helps.
nstuart
February 14, 2020, 4:02pm
16
Hi Rick,
I was running through terminal in bash, it seems that putting it into a shell script runs it properly!
My only problem now if that I am getting the following error:
I ran the following command"
and I got the following output:
Dataset File: p03_DN+tlrc
Identifier Code: AFN_LrcZ5Vby_BaalJjYB0I_Iw Creation Date: Thu Aug 1 11:56:38 2019
Template Space: TLRC
Dataset Type: Intensity (-fim)
Byte Order: LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode: BRIK
Storage Space: 18,573,604 (19 million) bytes
Geometry String: "MATRIX(1,0,0,-80,0,1,0,-80,0,0,1,-65):161,191,151"
Data Axes Tilt: Plumb
Data Axes Orientation:
first (x) = Right-to-Left
second (y) = Anterior-to-Posterior
third (z) = Inferior-to-Superior [-orient RAI]
R-to-L extent: -80.000 [R] -to- 80.000 [L] -step- 1.000 mm [161 voxels]
A-to-P extent: -80.000 [A] -to- 110.000 [P] -step- 1.000 mm [191 voxels]
I-to-S extent: -65.000 [I] -to- 85.000 [S] -step- 1.000 mm [151 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '#0' datum type is float: -2.71249 to 6.62421
How should I address this problem?
Thank you so much for all your help,
rickr
February 14, 2020, 5:43pm
17
Hi Nicole,
That is good news! Well, and bad about the mismatch…
What does this show?
3dinfo -d3 -n4 -prefix p*.HEAD
If the axes are different, it is good to back up and find out why. You might need to force things during the preprocessing.
nstuart
February 27, 2020, 3:36pm
18
Hi Rick,
Sorry for the late response (it was reading week at my university so I was away from this computer). That command has the following output:
1.000000 1.000000 1.000000 161 191 151 1 p03_DL
1.000000 1.000000 1.000000 161 191 151 1 p03_DN
1.000000 1.000000 1.000000 161 191 151 1 p03_DW
1.000000 1.000000 1.000000 161 191 151 1 p03_LN
1.000000 1.000000 1.000000 161 191 151 1 p03_LW
1.000000 1.000000 1.000000 161 191 151 1 p03_WN
1.000000 1.000000 1.000000 161 191 151 1 p04_DL
1.000000 1.000000 1.000000 161 191 151 1 p04_DN
1.000000 1.000000 1.000000 161 191 151 1 p04_DW
1.000000 1.000000 1.000000 161 191 151 1 p04_LN
1.000000 1.000000 1.000000 161 191 151 1 p04_LW
1.000000 1.000000 1.000000 161 191 151 1 p04_WN
1.000000 1.000000 1.000000 161 191 151 1 p05_DL
1.000000 1.000000 1.000000 161 191 151 1 p05_DN
1.000000 1.000000 1.000000 161 191 151 1 p05_DW
1.000000 1.000000 1.000000 161 191 151 1 p05_LN
1.000000 1.000000 1.000000 161 191 151 1 p05_LW
1.000000 1.000000 1.000000 161 191 151 1 p05_WN
1.000000 1.000000 1.000000 161 191 151 1 p06_DL
1.000000 1.000000 1.000000 161 191 151 1 p06_DN
1.000000 1.000000 1.000000 161 191 151 1 p06_DW
1.000000 1.000000 1.000000 161 191 151 1 p06_LN
1.000000 1.000000 1.000000 161 191 151 1 p06_LW
1.000000 1.000000 1.000000 161 191 151 1 p06_WN
1.000000 1.000000 1.000000 161 191 151 1 p07_DL
1.000000 1.000000 1.000000 161 191 151 1 p07_DN
1.000000 1.000000 1.000000 161 191 151 1 p07_DW
1.000000 1.000000 1.000000 161 191 151 1 p07_LN
1.000000 1.000000 1.000000 161 191 151 1 p07_LW
1.000000 1.000000 1.000000 161 191 151 1 p07_WN
1.000000 1.000000 1.000000 161 191 151 1 p08_DL
1.000000 1.000000 1.000000 161 191 151 1 p08_DN
1.000000 1.000000 1.000000 161 191 151 1 p08_DW
1.000000 1.000000 1.000000 161 191 151 1 p08_LN
1.000000 1.000000 1.000000 161 191 151 1 p08_LW
1.000000 1.000000 1.000000 161 191 151 1 p08_WN
1.000000 1.000000 1.000000 161 191 151 1 p09_DL
1.000000 1.000000 1.000000 161 191 151 1 p09_DN
1.000000 1.000000 1.000000 161 191 151 1 p09_DW
1.000000 1.000000 1.000000 161 191 151 1 p09_LN
1.000000 1.000000 1.000000 161 191 151 1 p09_LW
1.000000 1.000000 1.000000 161 191 151 1 p09_WN
1.000000 1.000000 1.000000 161 191 141 1 p101_DL
1.000000 1.000000 1.000000 161 191 141 1 p101_DN
1.000000 1.000000 1.000000 161 191 141 1 p101_DW
1.000000 1.000000 1.000000 161 191 141 1 p101_LN
1.000000 1.000000 1.000000 161 191 141 1 p101_LW
1.000000 1.000000 1.000000 161 191 141 1 p101_WN
1.000000 1.000000 1.000000 161 191 151 1 p10_DL
1.000000 1.000000 1.000000 161 191 151 1 p10_DN
1.000000 1.000000 1.000000 161 191 151 1 p10_DW
1.000000 1.000000 1.000000 161 191 151 1 p10_LN
1.000000 1.000000 1.000000 161 191 151 1 p10_LW
1.000000 1.000000 1.000000 161 191 151 1 p10_WN
1.000000 1.000000 1.000000 161 191 151 1 p11_DL
1.000000 1.000000 1.000000 161 191 151 1 p11_DN
1.000000 1.000000 1.000000 161 191 151 1 p11_DW
1.000000 1.000000 1.000000 161 191 151 1 p11_LN
1.000000 1.000000 1.000000 161 191 151 1 p11_LW
1.000000 1.000000 1.000000 161 191 151 1 p11_WN
1.000000 1.000000 1.000000 161 191 151 1 p14_DL
1.000000 1.000000 1.000000 161 191 151 1 p14_DN
1.000000 1.000000 1.000000 161 191 151 1 p14_DW
1.000000 1.000000 1.000000 161 191 151 1 p14_LN
1.000000 1.000000 1.000000 161 191 151 1 p14_LW
1.000000 1.000000 1.000000 161 191 151 1 p14_WN
1.000000 1.000000 1.000000 161 191 151 1 p15_DL
1.000000 1.000000 1.000000 161 191 151 1 p15_DN
1.000000 1.000000 1.000000 161 191 151 1 p15_DW
1.000000 1.000000 1.000000 161 191 151 1 p15_LN
1.000000 1.000000 1.000000 161 191 151 1 p15_LW
1.000000 1.000000 1.000000 161 191 151 1 p15_WN
1.000000 1.000000 1.000000 161 191 151 1 p16_DL
1.000000 1.000000 1.000000 161 191 151 1 p16_DN
1.000000 1.000000 1.000000 161 191 151 1 p16_DW
1.000000 1.000000 1.000000 161 191 151 1 p16_LN
1.000000 1.000000 1.000000 161 191 151 1 p16_LW
1.000000 1.000000 1.000000 161 191 151 1 p16_WN
1.000000 1.000000 1.000000 161 191 151 1 p17_DL
1.000000 1.000000 1.000000 161 191 151 1 p17_DN
1.000000 1.000000 1.000000 161 191 151 1 p17_DW
1.000000 1.000000 1.000000 161 191 151 1 p17_LN
1.000000 1.000000 1.000000 161 191 151 1 p17_LW
1.000000 1.000000 1.000000 161 191 151 1 p17_WN
1.000000 1.000000 1.000000 161 191 151 1 p18_DL
1.000000 1.000000 1.000000 161 191 151 1 p18_DN
1.000000 1.000000 1.000000 161 191 151 1 p18_DW
1.000000 1.000000 1.000000 161 191 151 1 p18_LN
1.000000 1.000000 1.000000 161 191 151 1 p18_LW
1.000000 1.000000 1.000000 161 191 151 1 p18_WN
1.000000 1.000000 1.000000 161 191 151 1 p19_DL
1.000000 1.000000 1.000000 161 191 151 1 p19_DN
1.000000 1.000000 1.000000 161 191 151 1 p19_DW
1.000000 1.000000 1.000000 161 191 151 1 p19_LN
1.000000 1.000000 1.000000 161 191 151 1 p19_LW
1.000000 1.000000 1.000000 161 191 151 1 p19_WN
1.000000 1.000000 1.000000 161 191 151 1 p20_DL
1.000000 1.000000 1.000000 161 191 151 1 p20_DN
1.000000 1.000000 1.000000 161 191 151 1 p20_DW
1.000000 1.000000 1.000000 161 191 151 1 p20_LN
1.000000 1.000000 1.000000 161 191 151 1 p20_LW
1.000000 1.000000 1.000000 161 191 151 1 p20_WN
1.000000 1.000000 1.000000 161 191 151 1 p21_DL
1.000000 1.000000 1.000000 161 191 151 1 p21_DN
1.000000 1.000000 1.000000 161 191 151 1 p21_DW
1.000000 1.000000 1.000000 161 191 151 1 p21_LN
1.000000 1.000000 1.000000 161 191 151 1 p21_LW
1.000000 1.000000 1.000000 161 191 151 1 p21_WN
Thank you!
Nicole
nstuart
February 27, 2020, 4:34pm
19
Hi Rick,
Another thing of note, I tested out removing the participant to see if it ran otherwise, and I get the same axes mismatch error for p04_DN.tlrc
I just want to let you know in case that changes the interpretation of the previously posted output. Is there possibly something in the “DN” comparison that you can see?
For reference, I get the following output about the data set dimensions:
Thank you!
rickr
February 27, 2020, 6:53pm
20
The dimensions need to match those of the first dataset. But if all the datasets are the same, it should be okay.
There should be text output that says, “Data set dimensions: nx = …”. Can you find that? What does it show?
Thanks,
– rick