Hi discoraj,
1) There was an error when I ran ClustExp_StatParse.py. And I don't know what the outputs mean:
...
Resampling master to subject data.
-- will fix any bad char check errors in /media/data/MyOutput_CleanSubjTab.1D
** non-Unix check output file '/media/data/MyOutput_CleanSubjTab.1D' exists, will overwrite
-- will fix any non-Unix check errors in /media/data/MyOutput_CleanSubjTab.1D
Traceback (most recent call last):
File "/home/data/abin/ClustExp_StatParse.py", line 407, in <module>
subj_dset_tab.append([fields[0],fields[2]])
IndexError: list index out of range
The code I used are:
ClustExp_StatParse.py \
-StatDSET box_ttest+tlrc \
-MeanBrik 0 \
-ThreshBrik 1 \
-SubjDSET All_My_Subj.nii.gz \
-SubjTable table.csv \
-master /media/data/TT_N27+tlrc
The table.csv:
sub001 sub001.results/stats.sub001_REML+tlrc[1] sub001.results/stats.sub001_REML+tlrc[1]
sub001 sub001.results/stats.sub001_REML+tlrc[4] sub001.results/stats.sub001_REML+tlrc[4]
sub002 sub002.results/stats.sub002_REML+tlrc[1] sub002.results/stats.sub002_REML+tlrc[1]
sub002 sub002.results/stats.sub002_REML+tlrc[4] sub002.results/stats.sub002_REML+tlrc[4]
sub003 sub003.results/stats.sub003_REML+tlrc[1] sub003.results/stats.sub003_REML+tlrc[1]
sub003 sub003.results/stats.sub003_REML+tlrc[4] sub003.results/stats.sub003_REML+tlrc[4]
sub004 sub004.results/stats.sub004_REML+tlrc[1] sub004.results/stats.sub004_REML+tlrc[1]
sub004 sub004.results/stats.sub004_REML+tlrc[4] sub004.results/stats.sub004_REML+tlrc[4]
sub005 sub005.results/stats.sub005_REML+tlrc[1] sub005.results/stats.sub005_REML+tlrc[1]
sub005 sub005.results/stats.sub005_REML+tlrc[4] sub005.results/stats.sub005_REML+tlrc[4]
sub006 sub006.results/stats.sub006_REML+tlrc[1] sub006.results/stats.sub006_REML+tlrc[1]
sub006 sub006.results/stats.sub006_REML+tlrc[4] sub006.results/stats.sub006_REML+tlrc[4]
sub007 sub007.results/stats.sub007_REML+tlrc[1] sub007.results/stats.sub007_REML+tlrc[1]
sub007 sub007.results/stats.sub007_REML+tlrc[4] sub007.results/stats.sub007_REML+tlrc[4]
And All_My_Subj.nii.gz:
3dinfo -verb All_My_Subj.nii.gz
++ 3dinfo: AFNI version=AFNI_18.0.02 (Jan 10 2018) [64-bit]
Dataset File: All_My_Subj.nii.gz
Identifier Code: AFN_-S-e78_FXiL7GWL6dh4Gbg Creation Date: Fri Jan 12 23:32:01 2018
Template Space: TT_N27
Dataset Type: Echo Planar (-epan)
Byte Order: LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode: NIFTI
Storage Space: 9,676,800 (10 million [mega]) bytes
Geometry String: "MATRIX(3,0,0,-79.5,0,3,0,-79.5,0,0,3,-63.5):54,64,50"
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: -79.500 [R] -to- 79.500 [L] -step- 3.000 mm [ 54 voxels]
A-to-P extent: -79.500 [A] -to- 109.500 [P] -step- 3.000 mm [ 64 voxels]
I-to-S extent: -63.500 -to- 83.500 [S] -step- 3.000 mm [ 50 voxels]
Number of time steps = 14 Time step = 1.00000s Origin = 0.00000s
-- At sub-brick #0 'sub001' datum type is float: -11.9993 to 17.5647
-- At sub-brick #1 'sub001' datum type is float: -16.8132 to 18.0239
-- At sub-brick #2 'sub002' datum type is float: -13.7661 to 6.53791
-- At sub-brick #3 'sub002' datum type is float: -18.4548 to 11.5191
-- At sub-brick #4 'sub003' datum type is float: -19.1143 to 10.8273
-- At sub-brick #5 'sub003' datum type is float: -9.07329 to 5.96413
-- At sub-brick #6 'sub004' datum type is float: -6.55489 to 6.34929
-- At sub-brick #7 'sub004' datum type is float: -15.9532 to 5.78403
-- At sub-brick #8 'sub005' datum type is float: -7.85877 to 21.545
-- At sub-brick #9 'sub005' datum type is float: -11.0492 to 16.6702
-- At sub-brick #10 'sub006' datum type is float: -7.49449 to 7.94652
-- At sub-brick #11 'sub006' datum type is float: -10.1083 to 12.1575
-- At sub-brick #12 'sub007' datum type is float: -19.5165 to 33.166
-- At sub-brick #13 'sub007' datum type is float: -21.4625 to 28.2601
----- HISTORY -----
[data@data-Inspiron-7570: Fri Jan 12 23:32:01 2018] {AFNI_18.0.02:linux_ubuntu_16_64} 3dcopy delete.me00.nii.gz All_My_Subj.nii.gz
2)There was also something wrong when I ran @ClustExp_run_shiny：
...
Attaching package: ‘shinydashboard’
The following object is masked from ‘package:graphics’:
box
Error in library(plotly) : there is no package called ‘plotly’
Calls: <Anonymous> ... sourceUTF8 -> eval -> eval -> ..stacktraceon.. -> library
停止执行（stopping execution ）
I think this error was caused by inappropriately installing some necessary R libraries. Because there were lots of warning messages when the command @afni_R_package_install - shiny was executed:
...
下载的程序包在
‘/tmp/RtmpMEWPwg/downloaded_packages’里(Downloaded packages are in ‘/tmp/RtmpMEWPwg/downloaded_packages’)
Warning messages:
1: In install.packages(c("shiny", "shinydashboard", "plotly", "colourpicker", :
安装程序包‘openssl’时退出狀態的值不是0 (The value of the exit state when installing the package 'openssl' is not 0 )
2: In install.packages(c("shiny", "shinydashboard", "plotly", "colourpicker", :
安装程序包‘httr’时退出狀態的值不是0 (The value of the exit state when installing the package 'httr' is not 0 )
3: In install.packages(c("shiny", "shinydashboard", "plotly", "colourpicker", :
安装程序包‘plotly’时退出狀態的值不是0 (The value of the exit state when installing the package 'shiny' is not 0 )
But I don't know how to fix these problems.
Could you help me?
Thank you in advance!
Edited 8 time(s). Last edit at 01/13/2018 09:55AM by Ren Po.
