afni.nimh.nih.gov
AFNI Message Board
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
| January 04, 2017 08:43AM | |
Hello AFNI peeps -
I have a stats file with a brick containing the contrast between two conditions (NOV and NUM). I can threshold the Tstat (p < .001) and cluster correct it (cluster size = 20) and when I generate the report the list of clusters will have the alpha probability values for each cluster on the right-hand side:
So far so good. But now I want to make a mask of only one side of this contrast (NOV>NUM) so I do this same process, except I also check the "Pos?" checkbox, to get rid of the NUM>NOV activations. Now when I generate the report only the positive clusters show up, as desired, but the alpha values are lost:
I can save this mask (via SaveMsk) and reload it and the mask seems to be what I want; but the absence of the alphas maked me worried that I'm doing something wrong or weird here. My 3drefit command is basically standard, aside from some scripting to allow me to automate for use with different masks and datasets:
and all appropriate .niml files have been created with 3dClustSim. From looking at the output of the processing pipeline, everything seems fine, no errors.
Can anyone explain where the alphas go, or if there's a more appropriate/correct way of doing what I want to do? I'm using all AFNI tools from version 16.3.19.
Thanks for any advice,
S
I have a stats file with a brick containing the contrast between two conditions (NOV and NUM). I can threshold the Tstat (p < .001) and cluster correct it (cluster size = 20) and when I generate the report the list of clusters will have the alpha probability values for each cluster on the right-hand side:
So far so good. But now I want to make a mask of only one side of this contrast (NOV>NUM) so I do this same process, except I also check the "Pos?" checkbox, to get rid of the NUM>NOV activations. Now when I generate the report only the positive clusters show up, as desired, but the alpha values are lost:
I can save this mask (via SaveMsk) and reload it and the mask seems to be what I want; but the absence of the alphas maked me worried that I'm doing something wrong or weird here. My 3drefit command is basically standard, aside from some scripting to allow me to automate for use with different masks and datasets:
3drefit \
-atrstring AFNI_CLUSTSIM_MASK file:${clustDir}/clustsim.${funcType}.${maskName}.mask \
-atrstring AFNI_CLUSTSIM_NN1_2sided file:${clustDir}/clustsim.${funcType}.${maskName}.NN1_1sided.niml \
-atrstring AFNI_CLUSTSIM_NN2_2sided file:${clustDir}/clustsim.${funcType}.${maskName}.NN2_1sided.niml \
-atrstring AFNI_CLUSTSIM_NN3_2sided file:${clustDir}/clustsim.${funcType}.${maskName}.NN3_1sided.niml \
-atrstring AFNI_CLUSTSIM_NN1_2sided file:${clustDir}/clustsim.${funcType}.${maskName}.NN1_2sided.niml \
-atrstring AFNI_CLUSTSIM_NN2_2sided file:${clustDir}/clustsim.${funcType}.${maskName}.NN2_2sided.niml \
-atrstring AFNI_CLUSTSIM_NN3_2sided file:${clustDir}/clustsim.${funcType}.${maskName}.NN3_2sided.niml \
-atrstring AFNI_CLUSTSIM_NN1_2sided file:${clustDir}/clustsim.${funcType}.${maskName}.NN1_bisided.niml \
-atrstring AFNI_CLUSTSIM_NN2_2sided file:${clustDir}/clustsim.${funcType}.${maskName}.NN2_bisided.niml \
-atrstring AFNI_CLUSTSIM_NN2_2sided file:${clustDir}/clustsim.${funcType}.${maskName}.NN3_bisided.niml \
${statsFile}
and all appropriate .niml files have been created with 3dClustSim. From looking at the output of the processing pipeline, everything seems fine, no errors.
Can anyone explain where the alphas go, or if there's a more appropriate/correct way of doing what I want to do? I'm using all AFNI tools from version 16.3.19.
Thanks for any advice,
S
| Subject | Author | Posted |
|---|---|---|
|
shanusmagnus | January 04, 2017 08:43AM |
|
jyaros | April 13, 2020 05:22PM |
