Hi,
In my project, I have found some voxel-clusters which have shown significant difference between Group A and Group B (at the p-value level about 0.01 in those voxel clusters). But after multiple comparison (e.g. FDR) for all 67000 voxels , the p-value of those voxel-clusters are more than 0.05.
I try to use 3dttest++ to do the cluster-level (e.g define 69 voxels as a clusters) multiple comparison for my p-values. Can someone help me about it?
Thank you very much,
Feng
after multiple comparison (e.g. FDR) for all 67000 voxels , the p-value of those voxel-clusters are more than 0.05.
I guess you meant the FDR q-value. FDR correction is relatively conservative most of the time.
I try to use 3dttest++ to do the cluster-level (e.g define 69 voxels as a clusters) multiple comparison
for my p-values. Can someone help me about it?
Two options: 1) use option -Clustsim, or 2) use option -ETAC. Read the help for more details.
Highly appreciate your help, Gang.
When I tried to do the cluster based t_test, I enter the following scripts, and got the error as bottom part. Would you please help me about this error? Thank you very much.
Best,
Feng
scripts:
3dttest++ -no1sam -nomeans -mask …/mask_map.nii -ClustSim -prefix …/t_test_alff.nii
-setA sub001.nii
sub002.nii
sub003.nii
sub004.nii
sub005.nii
sub006.nii
sub007.nii
sub008.nii
sub009.nii
sub010.nii
sub011.nii
sub013.nii
sub014.nii
sub015.nii
sub016.nii
sub017.nii
sub018.nii
sub019.nii
sub020.nii
sub021.nii
sub022.nii
sub023.nii
sub024.nii
sub025.nii
sub026.nii
sub027.nii
sub028.nii
sub029.nii
sub030.nii
sub031.nii
sub032.nii
sub033.nii
sub034.nii
sub035.nii
sub036.nii
sub037.nii
sub038.nii
sub039.nii
sub040.nii
-setB hc001.nii
hc002.nii
hc003.nii
hc004.nii
hc005.nii
hc006.nii
hc007.nii
hc008.nii
hc009.nii
hc010.nii
hc011.nii
hc012.nii
hc013.nii
hc014.nii
hc015.nii
hc016.nii
hc017.nii
hc018.nii
hc019.nii
hc020.nii
hc021.nii
hc022.nii
hc023.nii
hc024.nii
hc025.nii
hc027.nii
hc028.nii \
error:
++ 3dttest++: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
++ Authored by: Zhark++
** WARNING: NIfTI file …/mask_map.nii dimensions altered since AFNI extension was added
*+ WARNING: file …/mask_map.nii: corrected 203968 float errors
++ 67665 voxels in -mask dataset
++ Number of -clustsim threads set to 20
Fatal Signal 11 (SIGSEGV) received
EDIT_empty_copy
THD_open_tcat
THD_open_dataset
3dttest++ main
Bottom of Debug Stack
** Command line was:
3dttest++ -no1sam -nomeans -mask …/mask_map.nii -ClustSim -prefix …/t_test_alff.nii -setA sub001.nii sub002.nii sub003.nii sub004.nii sub005.nii sub006.nii sub007.nii sub008.nii sub009.nii sub010.nii sub011.nii sub013.nii sub014.nii sub015.nii sub016.nii sub017.nii sub018.nii sub019.nii sub020.nii sub021.nii sub022.nii sub023.nii sub024.nii sub025.nii sub026.nii sub027.nii sub028.nii sub029.nii sub030.nii sub031.nii sub032.nii sub033.nii sub034.nii sub035.nii sub036.nii sub037.nii sub038.nii sub039.nii sub040.nii -setB hc001.nii hc002.nii hc003.nii hc004.nii hc005.nii hc006.nii hc007.nii hc008.nii hc009.nii hc010.nii hc011.nii hc012.nii hc013.nii hc014.nii hc015.nii hc016.nii hc017.nii hc018.nii hc019.nii hc020.nii hc021.nii hc022.nii hc023.nii hc024.nii hc025.nii hc027.nii hc028.nii ’ ’
** AFNI version = AFNI_16.3.05 Compile date = Oct 24 2016
** [[Precompiled binary linux_openmp_64: Oct 24 2016]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Memory usage: chunks=3844 bytes=1756426
** Crash log is appended to file /home/fhan/.afni.crashlog
Hi Feng,
If you are modifying the NIFTI datasets after AFNI has read
them, then as the warnings suggest, the AFNI extensions
should be removed at that point. To do so after the fact,
consdier: nifti_tool -rm_ext ALL
Note that the crash might then be because the dimensions
differ across the datasets.
Thank you very much, Rick.
And after I removed AFNI extensions for all my data, those warnings about extension has gone.
But, there is an warning as:
++ 3dttest++: AFNI version=AFNI_16.3.05 (Oct 24 2016) [64-bit]
++ Authored by: Zhark++
*+ WARNING: file mask_map.nii: corrected 203968 float errors
++ 67665 voxels in -mask dataset
++ Number of -clustsim threads set to 20
Fatal Signal 11 (SIGSEGV) received
EDIT_empty_copy
THD_open_tcat
THD_open_dataset
3dttest++ main
Bottom of Debug Stack
** Command line was:
3dttest++ -no1sam -nomeans -zskip -mask mask_map.nii -ClustSim -prefix …/t_test_alff -setA sub001.nii sub002.nii sub003.nii sub004.nii sub005.nii sub006.nii sub007.nii sub008.nii sub009.nii sub010.nii sub011.nii sub013.nii sub014.nii sub015.nii sub016.nii sub017.nii sub018.nii sub019.nii sub020.nii sub021.nii sub022.nii sub023.nii sub024.nii sub025.nii sub026.nii sub027.nii sub028.nii sub029.nii sub030.nii sub031.nii sub032.nii sub033.nii sub034.nii sub035.nii sub036.nii sub037.nii sub038.nii sub039.nii sub040.nii -setB hc001.nii hc002.nii hc003.nii hc004.nii hc005.nii hc006.nii hc007.nii hc008.nii hc009.nii hc010.nii hc011.nii hc012.nii hc013.nii hc014.nii hc015.nii hc016.nii hc017.nii hc018.nii hc019.nii hc020.nii hc021.nii hc022.nii hc023.nii hc024.nii hc025.nii hc027.nii hc028.nii ’ ’
** AFNI version = AFNI_16.3.05 Compile date = Oct 24 2016
** [[Precompiled binary linux_openmp_64: Oct 24 2016]]
** Program Death **
Could you guide me about the float errors correction?
Thanks,
Feng
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