Group comparisons after 3dRegAna

sytang317 · July 27, 2020, 7:54pm

Hello, I need some help about 3dRegAna. I am doing a two-way ANOVA with unbalanced data. Below is a sample of my model (columns are factor a, factor b, and axb respectively).
3dRegAna
-rows 39
-cols 3
-xydata 0 0 0 subj1.nii
-xydata 0 1 0 subj2.nii
-xydata 1 0 0 subj3.nii
-xydata 1 1 1 subj4.nii
…
-model 1 2 3 : 0 \

I observed significant axb interaction at a couple of voxel clusters. So, I hope to perform pairwise comparisons to find out the detail. Any suggestion on how to do it?

Thanks!

Gang · July 28, 2020, 4:15pm

Use 3dMVM instead of 3dRegAna because the former is more equipped for teasing apart various effects.

sytang317 · July 29, 2020, 4:04pm

Thank you, Gang.

I tried to run 3dMVM but got the following error message:

** Error:
Illegal parameters on command line:
c(“-prefix 3dMVM_test -jobs 1 -bsVars ’AB’ -mask mask.nii -SS_type 3 -num_glt 2 -gltLabel 1 a1_b1_vs_b2 -gltCode 1 ‘A : 1a1 B : 1b1 -1b2’ -gltLabel 2 a2_b1_vs_b2 -gltCode 2 ‘A : 1a2 B : 1b1 -1*b2’ -dataTable”, “@table.txt”)
Try -allowed_options, or -help for details

I would appreciate some advice.

Thanks!
Shiyu

Gang · July 29, 2020, 8:34pm

Shiyu, could you show us the 3dMVM script? And how did you execute the script?

sytang317 · July 29, 2020, 9:06pm

Hi Gang, my script is below:
3dMVM -prefix 3dMVM_test -jobs 1
-bsVars 'AB’
-mask mask.nii
-SS_type 3
-num_glt 2
-gltLabel 1 a1_b1_vs_b2 -gltCode 1 ‘A : 1a1 B : 1b1 -1b2’
-gltLabel 2 a2_b1_vs_b2 -gltCode 2 ‘A : 1a2 B : 1b1 -1*b2’
-dataTable @table.txt

And the table.txt looks like this:
Subj A B InputFile
CD1 a1 b1 CD1_zmap.nii
CD2 a2 b2 CD2_zmap.nii
…

Thanks
Shiyu

Gang · July 30, 2020, 2:53pm

Again, how did you execute your 3dMVM script?

sytang317 · July 30, 2020, 5:56pm

I directly copied the command lines into the terminal.

sytang317 · July 30, 2020, 6:03pm

And the R version is 3.4.4. Not sure if it is relevant to this problem.

Gang · July 30, 2020, 10:12pm

Try to save the script to a file and then execute by typing something like

nohup tcsh myScript > myDiary &

See if you still get the error message.

sytang317 · July 31, 2020, 2:16pm

Hi Gang,

I tried to save the script to txt and execute it in terminal. But still got the same error:

** Error:
Illegal parameters on command line:
c(“-prefix 3dMVM_test -jobs 1”, “-bsVars AB", “-mask wbrainmask_th05.nii”, “-SS_type 3”, “-num_glt 2”, "-gltLabel 1 a1_b1_vs_b2 -gltCode 1 A : 1a1 B : 1b1-1b2”, “-gltLabel 2 a2_b1_vs_b2 -gltCode 2”, “A : 1a2 B : 1b1-1*b2”, “-dataTable @table_test.txt”)
Try -allowed_options, or -help for details

Again, the script I’m using is:
3dMVM -prefix 3dMVM_test -jobs 1 -bsVars ‘AB’ -mask mask.nii -SS_type 3 -num_glt 2 -gltLabel 1 a1_b1_vs_b2 -gltCode 1 'A : 1a1 B : 1b1-1b2’ -gltLabel 2 a2_b1_vs_b2 -gltCode 2 ‘A : 1a2 B : 1b1-1*b2’ -dataTable @table_test.txt

The table_test.txt is:
Subj A B InputFile
s1 a1 b1 s1_rest_z.nii
s2 a1 b1 s2_rest_z.nii
s3 a1 b1 s3_rest_z.nii
s4 a1 b1 s4_rest_z.nii
s5 a2 b2 s5_rest_z.nii
s6 a2 b2 s6_rest_z.nii
s7 a2 b2 s7_rest_z.nii
s8 a2 b2 s8_rest_z.nii
s9 a1 b2 s9_rest_z.nii
s10 a1 b2 s10_rest_z.nii
s11 a1 b2 s11_rest_z.nii
s12 a1 b2 s12_rest_z.nii
s13 a2 b1 s13_rest_z.nii
s14 a2 b1 s14_rest_z.nii
s15 a2 b1 s15_rest_z.nii
s16 a2 b1 s16_rest_z.nii

Gang · July 31, 2020, 3:31pm

I’m not so sure what’s going on about the situation since I can’t duplicate the error. A last ditch: what is your AFNI version? Is it up to date?

sytang317 · August 4, 2020, 8:24pm

Hi Gang,

I tried to type in the script directly into the terminal and the error did not show up. I think it could be some formatting issue of the text. However, it gave me this error:
** Error:
The number of -gltLabel is not consistent with that
specified by -num_glt 2

No matter how many glt I set, it always gave me the error saying the number is not consistent.

sytang317 · August 12, 2020, 6:51pm

Hi Gang,

I apologize for bothering you again… But I came across a new error message as below:

Error in outList[[1]][[n]] : subscript out of bounds
Calls: process.MVM.opts → gl_Constr
Execution halted

I think the issue is with the line below because everything works well without it.
-num_glt 1
-gltLabel 1 AvB -gltCode 1 ‘group : 1a -1b’ \

My data table looks like
-dataTable
Subj group treat InputFile
s1 a T1 s1_map_z.nii
s2 a T1 s2_map_z.nii
S3 a T2 s3_map_z.nii
S4 a T2 s4_map_z.nii
s5 b T1 s5_map_z.nii
s6 b T1 s6_map_z.nii
s7 b T2 s7_map_z.nii
s8 b T2 s8_map_z.nii

Could you help to see what could be wrong? Thanks.

Gang · August 13, 2020, 6:43pm

Can you show the whole 3dMVM script? Is it the same as before?


3dMVM -prefix 3dMVM_test -jobs 1 -bsVars  'A*B' -mask mask.nii -SS_type 3 -num_glt 2 -gltLabel 1 a1_b1_vs_b2 -gltCode 1 'A : 1*a1 B : 1*b1-1*b2' -gltLabel 2 a2_b1_vs_b2 -gltCode 2 'A : 1*a2 B : 1*b1-1*b2' -dataTable @table_test.txt

sytang317 · August 13, 2020, 7:01pm

Hi Gang, the whole script is:

3dMVM -prefix 3dmvm_test
-jobs 2
-mask brainmask.nii
-bsVars ‘grouptreat’
-num_glt 1
-gltLabel 1 AvB -gltCode 1 'group : 1a -1*b’
-dataTable
Subj group treat InputFile
s1 a T1 s1_map_z.nii
s2 a T1 s2_map_z.nii
S3 a T2 s3_map_z.nii
S4 a T2 s4_map_z.nii
s5 b T1 s5_map_z.nii
s6 b T1 s6_map_z.nii
s7 b T2 s7_map_z.nii
s8 b T2 s8_map_z.nii

It runs well without the glt lines:
-num_glt 1
-gltLabel 1 AvB -gltCode 1 ‘group : 1a -1b’ \

Many thanks!

Gang · August 14, 2020, 12:48pm

Since you’re not revealing your AFNI version, I suggest that you try a different interface:

https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/3dMVM_validator/main_toc.html

sytang317 · August 17, 2020, 6:26pm

Hi Gang,

Thank you so much for the suggestion. It works! I really appreciate your help.

Best,
Shiyu