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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:
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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
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Dear all,
I have run 3dFriedman to compare differences between processing/motion correction pipelines *; each pipeline has data from the same 8 subjects. The output gives me one brik for Chi-Square values, and another for the pipeline index (p1-p5).
How may I correct for multiple comparisons with the outputted dataset 'new_3dFriedman_FA_negative' ?
Thank you very much,
best wis
by
barbara
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AFNI Message Board
Great! Thanks!
This fixed it for good.
All the best,
Barbara
by
barbara
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AFNI Message Board
It works now, thank you so much!
I still have one slight problem though, I have to set the library paths every single time I want to run 3dAllineate or 3dQwarp.
neuro-222:~ NEURO-222$ echo 'export DYLD_FALLBACK_LIBRARY_PATH=$HOME/afni' >> .profile
neuro-222:~ NEURO-222$ echo 'export PATH=$PATH:$HOME/afni' >> .profile
neuro-222:~ NEURO-222$ . .profile
W
by
barbara
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AFNI Message Board
Dear Peter,
I had tried that already and the moving/renaming turned out not to work (with this error message sudo mv /usr/local/lib /usr/local/lib.save
mv: rename /usr/local/lib to /usr/local/lib.save/lib: No such file or directory
).
Dear Rick,
Thank you for answering, so here is the output of the file command.
file /Users/NEURO-222/afni/libg*
/Users/NEURO-222/afni/libgcc_s.1.dyli
by
barbara
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AFNI Message Board
Dear Peter,
Thanks again. This is the output.
otool -L /Users/NEURO-222/afni/3dAllineate
/Users/NEURO-222/afni/3dAllineate:
/usr/X11/lib/libXt.6.dylib (compatibility version 7.0.0, current version 7.0.0)
/usr/X11/lib/libfontconfig.1.dylib (compatibility version 6.0.0, current version 6.4.0)
/usr/lib/libiconv.2.dylib (compatibility version 7.0.0, current version 7.0.0)
/usr/X11/lib/
by
barbara
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AFNI Message Board
In the old window where I manually set the path etc. this is the output of the check
Things only work in the new window when I set the path manually again (but still the same library error).
Thanks ever so.
afni_system_check.py -check_all
============ afni_system_check.py version 0.6, March 14, 2014 ============
-------------------------------- general ---------------------------------
by
barbara
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AFNI Message Board
Dear Peter,
Thanks for your help. However, moving the lib to temp.lib did not help. I am still getting the same error message when running some of afni's programs like 3dQwarp and 3dAllineate
dyld: Library not loaded: /usr/local/lib/libgomp.1.dylib
Referenced from: /Users/NEURO-222/afni/3dQwarp
Reason: image not found
Trace/BPT trap: 5
Thanks,
Barbara
by
barbara
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AFNI Message Board
Dear Peter,
These are some outputs.
which afni
/Users/NEURO-222/afni/afni
NEURO-222:~ NEURO-222$ echo $DYLD_FALLBACK_LIBRARY_PATH
/Users/NEURO-222/afni
NEURO-222:~ NEURO-222$ 3dAllineate
dyld: Library not loaded: /usr/local/lib/libgomp.1.dylib
Referenced from: /Users/NEURO-222/afni/3dAllineate
Reason: image not found
Trace/BPT trap: 5
NEURO-222:~ NEURO-222$ 3dQwarp
dyld: Libr
by
barbara
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AFNI Message Board
This is the relevant part (for my OS) that uber_subject.py -help_install outputted after the afni_system_check.py -check_all
Thanks so much again.
B. OS X 10.6 (or later)
B1. via fink (assuming python 2.7 and the x11 version of qt4):
0. fink should be installed and current, to make current:
sudo fink selfupdate
1. install pyqt4 for python v
by
barbara
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AFNI Message Board
Dear Peter.
Thanks for looking into this. The output of the call you sent (afni_system_check.py -check_all) is:
(in the other following post I am going to paste the output of the call that was mentioned here in the output (uber_subject.py -help_install)
============ afni_system_check.py version 0.6, March 14, 2014 ============
-------------------------------- general -------------------
by
barbara
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AFNI Message Board
Dear ANFI experts,
I am wondering if 3dQwarp is expected to work on Mac Mavericks 10.9.2?
I have gotten these error messages and tried to solve the issue using comments of similar posts regarding earlier Mac OS like 10.8
They did not work for me though.
Please let me know if you have any suggestions.
Thanks a lot,
Barbara
dyld: lazy symbol binding failed: Symbol not found: ___emu
by
barbara
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AFNI Message Board
Dear Gang Chen,
Thanks ever so for your kind help.
I found a workaround by masking those voxels, now I am only ending up with those significant differences that truly originate from a comparison of at least two pipelines (and do not include the zeros).
Thanks a lot again!
I'd like to find out about the post-hoc comparison options in afni now. I'll have a look.
All the best,
Ba
by
barbara
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AFNI Message Board
Thank you very much for your answer.
Yes, I would like to treat those zeros as NaN if that is possible? Or is there a way of masking them out with the subrange option or something?
Thanks again.
Barbara
EDIT:
I have also been wondering about the output of non-integer numbers for the index sub-brik of both 3dKruskalWallis and 3dFriedmann. In the first volume I should see the index of the
by
barbara
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AFNI Message Board
Dear Gang Chen,
Thanks for your interest in my question.
My five DTI datasets with each 8 subjects originate from five different software pipelines with different processing steps turned on and off (say for instance the b-table rotation based on subject motion was done in one pipeline and omitted in the other).
I had 8 participants, so I processed their data in the same way for one pipeline
by
barbara
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AFNI Message Board
Dear AFNI experts,
I am looking to use the 3dKruskalWallis function for the comparisons of 5 different pipelines, could you please verify if this call is correct, if I would like to exclude any zero voxels in the comparison?
My data consists of 8 sub-briks for each of the five pipelines. I want to avoid that positive valued voxels are compared to zero valued voxels.
Thanks a bunch.
Best
by
barbara
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AFNI Message Board