Dear AFNI experts:
I met the ’ error : Inappropriate coding in test No.5! ’ when I run the script for 3dMVM.
There are two groups in my study: treatment group(also named alpha group) and ctrl group. There are both pre-test and post-test In each group, 13 subjects in alpha group and 9 subjects in ctrl group.
the script attached below:
3dMVM -prefix ~/Desktop/NFT_DTI_alpha/output/group_analysis/alpha_block_experiment -jobs 4
-bsVars Group
-wsVars Time
-num_glt 8
-gltLabel 1 alpha_pre -gltCode 1 ‘Group : 1* alpha Time: 1pre’
-gltLabel 2 alpha_post -gltCode 2 'Group : 1 alpha Time: 1post’
-gltLabel 3 ctrl_pre -gltCode 3 'Group : 1 ctrl Time: 1pre’
-gltLabel 4 ctrl_post -gltCode 4 'Group : 1ctrl Time: 1post’
-gltLabel 5 alphapost_vs_alphapre -gltCode 5 'Group : 1 alpha Time: 1post - 1pre’
-gltLabel 6 ctrlpost_vs_ctrlpre -gltCode 6 ‘Group : 1* ctrl Time: 1post - 1pre’
-gltLabel 7 alphapre_vs_ctrlpre -gltCode 7 ‘Group : 1* alpha - 1ctrl Time: 1pre’
-gltLabel 8 alphapost_vs_ctrlpost -gltCode 8 ‘Group : 1* alpha - 1ctrl Time: 1post’
-dataTable
Subj Group Time InputFile
a01 alpha pre ~/Desktop/NFT_DTI_alpha/output/00001/standard_space/NFT_a_00001_FA_4normalize_to_target_1mm.nii.gz
a01 alpha post ~/Desktop/NFT_DTI_alpha/output/00002/standard_space/NFT_a_00002_FA_4normalize_to_target_1mm.nii.gz
a02 alpha pre ~/Desktop/NFT_DTI_alpha/output/00003/standard_space/NFT_a_00003_FA_4normalize_to_target_1mm.nii.gz
a02 alpha post ~/Desktop/NFT_DTI_alpha/output/00004/standard_space/NFT_a_00004_FA_4normalize_to_target_1mm.nii.gz
a03 alpha pre ~/Desktop/NFT_DTI_alpha/output/00005/standard_space/NFT_a_00005_FA_4normalize_to_target_1mm.nii.gz
a03 alpha post ~/Desktop/NFT_DTI_alpha/output/00006/standard_space/NFT_a_00006_FA_4normalize_to_target_1mm.nii.gz
a04 alpha pre ~/Desktop/NFT_DTI_alpha/output/00007/standard_space/NFT_a_00007_FA_4normalize_to_target_1mm.nii.gz
a04 alpha post ~/Desktop/NFT_DTI_alpha/output/00008/standard_space/NFT_a_00008_FA_4normalize_to_target_1mm.nii.gz
a05 alpha pre ~/Desktop/NFT_DTI_alpha/output/00009/standard_space/NFT_a_00009_FA_4normalize_to_target_1mm.nii.gz
a05 alpha post ~/Desktop/NFT_DTI_alpha/output/00010/standard_space/NFT_a_00010_FA_4normalize_to_target_1mm.nii.gz
a06 alpha pre ~/Desktop/NFT_DTI_alpha/output/00011/standard_space/NFT_a_00011_FA_4normalize_to_target_1mm.nii.gz
a06 alpha post ~/Desktop/NFT_DTI_alpha/output/00012/standard_space/NFT_a_00012_FA_4normalize_to_target_1mm.nii.gz
a07 alpha pre ~/Desktop/NFT_DTI_alpha/output/00013/standard_space/NFT_a_00013_FA_4normalize_to_target_1mm.nii.gz
a07 alpha post ~/Desktop/NFT_DTI_alpha/output/00014/standard_space/NFT_a_00014_FA_4normalize_to_target_1mm.nii.gz
a08 alpha pre ~/Desktop/NFT_DTI_alpha/output/00015/standard_space/NFT_a_00015_FA_4normalize_to_target_1mm.nii.gz
a08 alpha post ~/Desktop/NFT_DTI_alpha/output/00016/standard_space/NFT_a_00016_FA_4normalize_to_target_1mm.nii.gz
a09 alpha pre ~/Desktop/NFT_DTI_alpha/output/00017/standard_space/NFT_a_00017_FA_4normalize_to_target_1mm.nii.gz
a09 alpha post ~/Desktop/NFT_DTI_alpha/output/00018/standard_spaceNFT_a_00018_FA_4normalize_to_target_1mm.nii.gz
a10 alpha pre ~/Desktop/NFT_DTI_alpha/output/00019/standard_space/NFT_a_00019_FA_4normalize_to_target_1mm.nii.gz
a10 alpha post ~/Desktop/NFT_DTI_alpha/output/00020/standard_space/NFT_a_00020_FA_4normalize_to_target_1mm.nii.gz
a11 alpha pre ~/Desktop/NFT_DTI_alpha/output/00021/standard_space/NFT_a_00021_FA_4normalize_to_target_1mm.nii.gz
a11 alpha post ~/Desktop/NFT_DTI_alpha/output/00022/standard_space/NFT_a_00022_FA_4normalize_to_target_1mm.nii.gz
a12 alpha pre ~/Desktop/NFT_DTI_alpha/output/00023/standard_space/NFT_a_00023_FA_4normalize_to_target_1mm.nii.gz
a12 alpha post ~/Desktop/NFT_DTI_alpha/output/00024/standard_space/NFT_a_00024_FA_4normalize_to_target_1mm.nii.gz
a13 alpha pre ~/Desktop/NFT_DTI_alpha/output/00025/standard_space/NFT_a_00025_FA_4normalize_to_target_1mm.nii.gz
a13 alpha post ~/Desktop/NFT_DTI_alpha/output/00026/standard_space/NFT_a_00026_FA_4normalize_to_target_1mm.nii.gz
c01 ctrl pre ~/Desktop/NFT_DTI_ctrl/output/00001/standard_space/NFT_c_00001_FA_4normalize_to_target_1mm.nii.gz
c01 ctrl post ~/Desktop/NFT_DTI_ctrl/output/00002/standard_space/NFT_c_00002_FA_4normalize_to_target_1mm.nii.gz
c02 ctrl pre ~/Desktop/NFT_DTI_ctrl/output/00003/standard_space/NFT_c_00003_FA_4normalize_to_target_1mm.nii.gz
c02 ctrl post ~/Desktop/NFT_DTI_ctrl/output/00004/standard_space/NFT_c_00004_FA_4normalize_to_target_1mm.nii.gz
c03 ctrl pre ~/Desktop/NFT_DTI_ctrl/output/00005/standard_space/NFT_c_00005_FA_4normalize_to_target_1mm.nii.gz
c03 ctrl post ~/Desktop/NFT_DTI_ctrl/output/00006/standard_space/NFT_c_00006_FA_4normalize_to_target_1mm.nii.gz
c04 ctrl pre ~/Desktop/NFT_DTI_ctrl/output/00007/standard_space/NFT_c_00007_FA_4normalize_to_target_1mm.nii.gz
c04 ctrl post ~/Desktop/NFT_DTI_ctrl/output/00008/standard_space/NFT_c_00008_FA_4normalize_to_target_1mm.nii.gz
c05 ctrl pre ~/Desktop/NFT_DTI_ctrl/output/00009/standard_space/NFT_c_00009_FA_4normalize_to_target_1mm.nii.gz
c05 ctrl post ~/Desktop/NFT_DTI_ctrl/output/00010/standard_spaceNFT_c_00010_FA_4normalize_to_target_1mm.nii.gz
c06 ctrl pre ~/Desktop/NFT_DTI_ctrl/output/00011/standard_space/NFT_c_00011_FA_4normalize_to_target_1mm.nii.gz
c06 ctrl post ~/Desktop/NFT_DTI_ctrl/output/00012/standard_space/NFT_c_00012_FA_4normalize_to_target_1mm.nii.gz
c07 ctrl pre ~/Desktop/NFT_DTI_ctrl/output/00013/standard_space/NFT_c_00013_FA_4normalize_to_target_1mm.nii.gz
c07 ctrl post ~/Desktop/NFT_DTI_ctrl/output/00014/standard_space/NFT_c_00014_FA_4normalize_to_target_1mm.nii.gz
c08 ctrl pre ~/Desktop/NFT_DTI_ctrl/output/00015/standard_space/NFT_c_00015_FA_4normalize_to_target_1mm.nii.gz
c08 ctrl post ~/Desktop/NFT_DTI_ctrl/output/00016/standard_space/NFT_c_00016_FA_4normalize_to_target_1mm.nii.gz
c09 ctrl pre ~/Desktop/NFT_DTI_ctrl/output/00017/standard_space/NFT_c_00017_FA_4normalize_to_target_1mm.nii.gz
c09 ctrl post ~/Desktop/NFT_DTI_ctrl/output/00018/standard_space/NFT_c_00018_FA_4normalize_to_target_1mm.nii.gz
And I run the command below in terminal:
afni_system_check.py -check_all
the results show that:
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 4.4.0-72-lowlatency
version: #93-Ubuntu SMP PREEMPT Fri Mar 31 15:25:21 UTC 2017
distribution: Ubuntu 16.04 xenial
number of CPUs: 8
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/fzshaw/abin/afni
afni version : Precompiled binary linux_openmp_64: Apr 12 2017
: AFNI_17.1.01
AFNI_version.txt : AFNI_17.1.01, linux_openmp_64, Apr 12 2017
which python : /usr/bin/python
python version : 2.7.12
which R : /usr/bin/R
R version : R version 3.3.3 (2017-03-06) – “Another Canoe”
which tcsh : /usr/bin/tcsh
instances of various programs found in PATH:
afni : 1 (/home/fzshaw/abin/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python2.7)
python2 : 1 (/usr/bin/python2.7)
python3 : 1 (/usr/bin/python3.5)
testing ability to start various programs…
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
checking for R packages…
rPkgsInstall -pkgs ALL -check : success
checking for $HOME files…
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
------------------------------ python libs -------------------------------
++ module ‘PyQt4’ found at /usr/lib/python2.7/dist-packages/PyQt4
++ module loaded: PyQt4
-------------------------------- env vars --------------------------------
PATH = /usr/local/fsl/bin:/usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/share/fsl/5.0/bin:/usr/lib/fsl/5.0:/usr/local/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/fzshaw/abin
PYTHONPATH =
R_LIBS = /home/fzshaw/R
LD_LIBRARY_PATH = /usr/lib/fsl/5.0
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: … [rickr]: updated FT_white.nii w/out 16 (brain stem)
data dir : found AFNI_demos under $HOME
top history: … [pault]: remove rank from FATCAT_DEMO, FAT_MVM_DEMO
data dir : found suma_demo under $HOME
top history: …/SUMA_data/Build_tmp on Wed Aug 20 10:04:23 EDT 2014
data dir : found afni_handouts under $HOME
atlas : found TT_N27+tlrc under /home/fzshaw/abin
atlas : found TT_N27+tlrc under /usr/share/afni/atlases
------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 1.2.19 (amd64)
have Ubuntu system: Ubuntu 16.04 xenial
========================= summary, please fix: =========================
- login shell ‘bash’, trusting user to translate from ‘tcsh’
- shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
looking forward to your reply, thanks~