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Dear AFNI users-
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely, AFNI HQ
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
https://discuss.afni.nimh.nih.gov
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely, AFNI HQ
| December 19, 2018 01:49AM | |
Hi,
This is my script:
=============
#!/bin/bash
#this function used for extracting the beta value of each interaction iterm each subject
cd /home/zhangxiaochu/zharj/igt_ddt/ddt
curr_path=`pwd`
output_path=$curr_path/interaction_regress
data_dir=$curr_path/function115
psycho1=all_hard
psycho2=all_easy
var_num=18
#var_num=15
var_num=13
var_name=allrun
cd $data_dir
sbname=`ls`;
cd $output_path
hard=""
for sb in $sbname;do
cd $curr_path/beta
hard="${hard}beta_${sb}_${psycho1}_${var_name}+tlrc ";
done
easy=""
for sb in $sbname;do
cd $curr_path/beta
easy="${easy}beta_${sb}_${psycho2}_${var_name}+tlrc ";
done
rm -f $curr_path/ttest_result/hard_easy*
#setA-setB
3dttest++ -prefix $curr_path/ttest_result/hard_easy -setA ${hard} -setB ${easy} -paired -Clustsim 6
==============
These are outputs in the command:
=========
++ 3dttest++: AFNI version=AFNI_18.2.03 (Jul 5 2018) [64-bit]
++ Authored by: Zhark++
++ option -setA :: processing as SHORT form (all values are datasets)
++ option -setB :: processing as SHORT form (all values are datasets)
++ Number of -Clustsim threads set to 6
+ Default clustsim prefix set to '/home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy'
++ no mask ==> processing all 196625 voxels
++ 2-sample test: '-AminusB' option is assumed
++ paired test: results will be SetA - SetB
++ loading -setA datasets
*+ WARNING: 3dttest++ -setA :: 117467 vectors are constant
++ loading -setB datasets
*+ WARNING: 3dttest++ -setB :: 117467 vectors are constant
++ Memory usage now = 380,648,963 (381 million [mega])
++ t-testing:0123456789.0123456789.0123456789.0123456789.0123456789.!
+ skipped 117467 voxels completely for having constant data
++ ---------- End of analyses -- freeing workspaces ----------
++ Memory usage now = 196,586,235 (197 million [mega])
++ Creating FDR curves in output dataset
++ Smallest FDR q [1 SetA-SetB_Zscr] = 1.02614e-13
++ Smallest FDR q [3 SetA_Zscr] = 1.67689e-14
++ Smallest FDR q [5 SetB_Zscr] = 4.08909e-13
+ Added 3 FDR curves to dataset
++ Output dataset /home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy+tlrc.BRIK
++ Output dataset /home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.resid.nii
+ paired test: results are SetA - SetB
++ ================ Starting -Clustsim calculations ================
+ === temporary files will have prefix /home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy ===
+ === running 6 -randomsign jobs (1667 iterations per job) ===
++ 3dttest++: AFNI version=AFNI_18.2.03 (Jul 5 2018) [64-bit]
++ Authored by: Zhark++
++ option -setA :: processing as SHORT form (all values are datasets)
++ option -setB :: processing as SHORT form (all values are datasets)
++ random seeds are 894883164 1209042429
++ no mask ==> processing all 196625 voxels
++ 2-sample test: '-AminusB' option is assumed
++ paired test: results will be SetA - SetB
++ loading -setA datasets
*+ WARNING: 3dttest++ -setA :: 117467 vectors are constant
++ loading -setB datasets
*+ WARNING: 3dttest++ -setB :: 117467 vectors are constant
++ Memory usage now = 185,534,595 (186 million [mega])
++ t-test randomsign:0123456789.0123456789.0123456789.0123456789.0123456789.0!
++ saving main effect t-stat MIN/MAX values in .//home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0000.minmax.1D
** ERROR: Can't open for output: .//home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0000.minmax.1D
++ ---------- End of analyses -- freeing workspaces ----------
++ Memory usage now = 1,311,769,263 (1.3 billion [giga])
** ERROR (nifti_image_write_hdr_img2): cannot open output file './/home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0000.nii'
+ paired test: results are SetA - SetB
++ ----- 3dttest++ says so long, farewell, and happy trails to you :) -----
+ 3dttest++ ===== simulation jobs have finished (909.7 s elapsed)
** ERROR: Can't read file .//home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0000.minmax.1D
** ERROR: Can't read file .//home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0001.minmax.1D
** ERROR: Can't read file .//home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0002.minmax.1D
** ERROR: Can't read file .//home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0003.minmax.1D
** ERROR: Can't read file .//home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0004.minmax.1D
** ERROR: Can't read file .//home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0005.minmax.1D
+ 3dttest++ ===== starting 3dClustSim A: elapsed = 926.6 s
++ 3dClustSim: AFNI version=AFNI_18.2.03 (Jul 5 2018) [64-bit]
++ Authored by: RW Cox and BD Ward
** ERROR (nifti_image_read): failed to find header file for './/home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0000.nii'
** ERROR: -inset './/home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0000.nii': failure to open dataset
** ERROR (nifti_image_read): failed to find header file for './/home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0001.nii'
** ERROR: -inset './/home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0001.nii': failure to open dataset
** ERROR (nifti_image_read): failed to find header file for './/home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0002.nii'
** ERROR: -inset './/home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0002.nii': failure to open dataset
** ERROR (nifti_image_read): failed to find header file for './/home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0003.nii'
** ERROR: -inset './/home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0003.nii': failure to open dataset
** ERROR (nifti_image_read): failed to find header file for './/home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0004.nii'
** ERROR: -inset './/home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0004.nii': failure to open dataset
** ERROR (nifti_image_read): failed to find header file for './/home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0005.nii'
** ERROR: -inset './/home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0005.nii': failure to open dataset
** FATAL ERROR: no valid datasets opened after -inset
** Program compile date = Jul 5 2018
** FATAL ERROR: ===== 3dClustSim command failed(( =====
** Program compile date = Jul 5 2018
=====================
AFNI is Precompiled binary linux_openmp_64: Jul 5 2018 (Version AFNI_18.2.03)
CENTOS is CentOS Linux release 7.3.1611 (Core)
Thanks
Best.
Rujing
This is my script:
=============
#!/bin/bash
#this function used for extracting the beta value of each interaction iterm each subject
cd /home/zhangxiaochu/zharj/igt_ddt/ddt
curr_path=`pwd`
output_path=$curr_path/interaction_regress
data_dir=$curr_path/function115
psycho1=all_hard
psycho2=all_easy
var_num=18
#var_num=15
var_num=13
var_name=allrun
cd $data_dir
sbname=`ls`;
cd $output_path
hard=""
for sb in $sbname;do
cd $curr_path/beta
hard="${hard}beta_${sb}_${psycho1}_${var_name}+tlrc ";
done
easy=""
for sb in $sbname;do
cd $curr_path/beta
easy="${easy}beta_${sb}_${psycho2}_${var_name}+tlrc ";
done
rm -f $curr_path/ttest_result/hard_easy*
#setA-setB
3dttest++ -prefix $curr_path/ttest_result/hard_easy -setA ${hard} -setB ${easy} -paired -Clustsim 6
==============
These are outputs in the command:
=========
++ 3dttest++: AFNI version=AFNI_18.2.03 (Jul 5 2018) [64-bit]
++ Authored by: Zhark++
++ option -setA :: processing as SHORT form (all values are datasets)
++ option -setB :: processing as SHORT form (all values are datasets)
++ Number of -Clustsim threads set to 6
+ Default clustsim prefix set to '/home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy'
++ no mask ==> processing all 196625 voxels
++ 2-sample test: '-AminusB' option is assumed
++ paired test: results will be SetA - SetB
++ loading -setA datasets
*+ WARNING: 3dttest++ -setA :: 117467 vectors are constant
++ loading -setB datasets
*+ WARNING: 3dttest++ -setB :: 117467 vectors are constant
++ Memory usage now = 380,648,963 (381 million [mega])
++ t-testing:0123456789.0123456789.0123456789.0123456789.0123456789.!
+ skipped 117467 voxels completely for having constant data
++ ---------- End of analyses -- freeing workspaces ----------
++ Memory usage now = 196,586,235 (197 million [mega])
++ Creating FDR curves in output dataset
++ Smallest FDR q [1 SetA-SetB_Zscr] = 1.02614e-13
++ Smallest FDR q [3 SetA_Zscr] = 1.67689e-14
++ Smallest FDR q [5 SetB_Zscr] = 4.08909e-13
+ Added 3 FDR curves to dataset
++ Output dataset /home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy+tlrc.BRIK
++ Output dataset /home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.resid.nii
+ paired test: results are SetA - SetB
++ ================ Starting -Clustsim calculations ================
+ === temporary files will have prefix /home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy ===
+ === running 6 -randomsign jobs (1667 iterations per job) ===
++ 3dttest++: AFNI version=AFNI_18.2.03 (Jul 5 2018) [64-bit]
++ Authored by: Zhark++
++ option -setA :: processing as SHORT form (all values are datasets)
++ option -setB :: processing as SHORT form (all values are datasets)
++ random seeds are 894883164 1209042429
++ no mask ==> processing all 196625 voxels
++ 2-sample test: '-AminusB' option is assumed
++ paired test: results will be SetA - SetB
++ loading -setA datasets
*+ WARNING: 3dttest++ -setA :: 117467 vectors are constant
++ loading -setB datasets
*+ WARNING: 3dttest++ -setB :: 117467 vectors are constant
++ Memory usage now = 185,534,595 (186 million [mega])
++ t-test randomsign:0123456789.0123456789.0123456789.0123456789.0123456789.0!
++ saving main effect t-stat MIN/MAX values in .//home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0000.minmax.1D
** ERROR: Can't open for output: .//home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0000.minmax.1D
++ ---------- End of analyses -- freeing workspaces ----------
++ Memory usage now = 1,311,769,263 (1.3 billion [giga])
** ERROR (nifti_image_write_hdr_img2): cannot open output file './/home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0000.nii'
+ paired test: results are SetA - SetB
++ ----- 3dttest++ says so long, farewell, and happy trails to you :) -----
+ 3dttest++ ===== simulation jobs have finished (909.7 s elapsed)
** ERROR: Can't read file .//home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0000.minmax.1D
** ERROR: Can't read file .//home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0001.minmax.1D
** ERROR: Can't read file .//home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0002.minmax.1D
** ERROR: Can't read file .//home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0003.minmax.1D
** ERROR: Can't read file .//home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0004.minmax.1D
** ERROR: Can't read file .//home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0005.minmax.1D
+ 3dttest++ ===== starting 3dClustSim A: elapsed = 926.6 s
++ 3dClustSim: AFNI version=AFNI_18.2.03 (Jul 5 2018) [64-bit]
++ Authored by: RW Cox and BD Ward
** ERROR (nifti_image_read): failed to find header file for './/home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0000.nii'
** ERROR: -inset './/home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0000.nii': failure to open dataset
** ERROR (nifti_image_read): failed to find header file for './/home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0001.nii'
** ERROR: -inset './/home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0001.nii': failure to open dataset
** ERROR (nifti_image_read): failed to find header file for './/home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0002.nii'
** ERROR: -inset './/home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0002.nii': failure to open dataset
** ERROR (nifti_image_read): failed to find header file for './/home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0003.nii'
** ERROR: -inset './/home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0003.nii': failure to open dataset
** ERROR (nifti_image_read): failed to find header file for './/home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0004.nii'
** ERROR: -inset './/home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0004.nii': failure to open dataset
** ERROR (nifti_image_read): failed to find header file for './/home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0005.nii'
** ERROR: -inset './/home/zhangxiaochu/zharj/igt_ddt/ddt/ttest_result/hard_easy.0005.nii': failure to open dataset
** FATAL ERROR: no valid datasets opened after -inset
** Program compile date = Jul 5 2018
** FATAL ERROR: ===== 3dClustSim command failed
(( =====
** Program compile date = Jul 5 2018
=====================
AFNI is Precompiled binary linux_openmp_64: Jul 5 2018 (Version AFNI_18.2.03)
CENTOS is CentOS Linux release 7.3.1611 (Core)
Thanks
Best.
Rujing
| Subject | Author | Posted |
|---|---|---|
|
charujing123 | December 19, 2018 01:49AM |
|
rick reynolds | December 19, 2018 09:12AM |
|
charujing123 | December 20, 2018 01:01AM |
