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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:
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
History of AFNI updates
Page 5 of 5
Pages: 12345
Results 121 - 143 of 143
Hi,
Wow that was fast.
I can wait for the binaries, no problem.
Thanks, Justin
by
discoraj
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AFNI Message Board
Hi,
I ran this code using the most update binaries on OSX 10.9.1:
3dQwarp -verb -prefix ${subj}.anat.uni.strip.mni.2in1 \
-duplo -useweight -blur 0 3 -base MNI_1mm_brain+tlrc -allineate \
-allineate_opts '-twopass -cost nmi -autoweight -fineblur 3 -cmass -source_automask -automask' \
-source ${subj}.anat.uni.strip+orig
Most of the output from -verb is for the 3DAllineate
by
discoraj
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AFNI Message Board
hi,
Just an update. I am still having the same problems with the 01/31 update.
Any word on what is going on?
thanks, Justin
by
discoraj
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AFNI Message Board
Hi,
Is it best to have a unifized anat as the input to 3dSeg or just the original anat?
thanks, Justin
by
discoraj
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AFNI Message Board
hi,
changing the 0 to 1 gives a close T value
cdf -v -p2t fico 0.001 69 1 1
t = 0.387606
but from the afni viewer it should be more like .3836
so I suppose its not correct
thanks, Justin
by
discoraj
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AFNI Message Board
Hi,
After generating a volume of type fico with 3dTcorrelate, the p2t always gives me zeros.
from 3dinfo:
statcode = fico; statpar = 69 1 0
The following commands give me zeros regardless of the p I input:
ccalc -expr "fico_p2t(0.001,69,1,0)"
or
cdf -v -p2t fico 0.001 69 1 0
The slider in the afni viewer works, but the "set p-value" dialog box gives zeros as w
by
discoraj
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AFNI Message Board
just an update:
I tried putting everything in the same directory (all permissions correct).
also tried images in afni not nifti format.
and with the 12/20 update.
still same error.
I am currently running with the separate 3dAllineate and that works fine for now.
thanks, Justin
by
discoraj
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AFNI Message Board
hi,
I still get the error with the updated binaries.
** FATAL ERROR: Can't open replacement source??
** Program compile date = Dec 16 2013
same issue.
thanks, Justin
by
discoraj
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AFNI Message Board
hi,
Does a talairach whole head template exist somewhere?
thanks, Justin
by
discoraj
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AFNI Message Board
Hi afni experts,
I am running into an error in 3dQwarp when adding the -allineate options.
the error is:
++ 3dQwarp: replacing source dataset with DBS.018.anat.uni.strip.mni.2in1_Allin.nii
** FATAL ERROR: Can't open replacement source??
This is the script that I am using:
3dQwarp -prefix ${subj}.anat.uni.strip.mni.2in1 \
-duplo -useweight -blur 0 3 -base ${MNI_1mm} -allineat
by
discoraj
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AFNI Message Board
Thanks,
I wanted to see the clusterize report, but I suppose it is not a common thing to drive.
thanks again, Justin
by
discoraj
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AFNI Message Board
Hi,
Is there anyway to get ANFI plugout_drive to set the clusterize and show the report?
thanks, Justin
by
discoraj
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AFNI Message Board
Hi,
I am running the 3dMVM for a 1-way 3 level (group) anova.
Afni is up to date, but I think the latest update changed something.
The output of 3dMVM now has sub brik "#0 (Intercept) F".
Also the sub brik "#1 group F" (as specified in the model), does not calculate the p-value in the afni main display gui.
It seems that the statpar for the intercept and the model are
by
discoraj
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AFNI Message Board
hi,
I am trying something a little funky and need some stats help.
Using resting state data, for each subject, I have a conjunction of 3 seed to whole brain maps.
This gives me a binary volume with 1 or 0 to say if that voxel is common to all 3 maps. I want to compare those binary volumes across groups. I am wondering if a chi-squared test is valid, and how afni could do it.
tldr vers
by
discoraj
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AFNI Message Board
Hi,
Thanks so much. That makes sense.
so...
Which should I use?
3dMVM GLT or 3dTtest++?
I suppose it depends on the question I am trying to answer.
thanks again everyone,
Justin
ps
Peter say hi to your brother for me. I sat next to him at the last afni bootcamp.
by
discoraj
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AFNI Message Board
Hi,
Sorry, the 3dttest++ should be 38 because a subset of the controls are used for that one (17).
My mistake on explaining that part.
But in the 3dMVM the degrees of freedom should be 23+27-2=48 for the ttest not 100?
thanks again, Justin
by
discoraj
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AFNI Message Board
Hi,
I am comparing them two groups at a time in 3dttest++.
The degrees of freedom are correct for the anova and the ttest separately, but I was not sure if they should be the same.
groups are 23,53,27 for the anova
and 23,27 for the ttest.
so 100 and 38 should be right for the respective tests.
thanks, Justin
by
discoraj
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AFNI Message Board
Hi,
I am running 3dMVM for a simple 1-way 3 group ANOVA and adding the post hoc ttests in the glt.
When I run the 3dMVM the fitt statpar for the ttest subbrik in the image header gives me degrees of freedom for the ANOVA, which differs from the fitt statpar if I run the same with 3dTtest++.
3dMVM
-- At sub-brick #4 'DBSvCon:t' datum type is float: -5.31884 to 4.1929
by
discoraj
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AFNI Message Board
Hi,
@AddEdge crashes on the +tlrc files. It looks for tmp_avg+orig instead of tmp_avg+tlrc.
I think I can resample or refit (can't remember which) to change the +tlrc to +orig, but that's a bit clunky.
thanks, Justin
by
discoraj
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AFNI Message Board
It is off to a good start!
Any thoughts on the @AddEdge for tlrc transforms?
thanks again, Justin
by
discoraj
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AFNI Message Board
Hi,
Am I missing something or is it not possible to use @AddEdge for the orig to tlrc transformation?
Also I am loving the speed and results from auto_warp.py but it needs file name editing to work correctly.
Is that safe to use at the moment?
thanks, Justin
by
discoraj
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AFNI Message Board
Page 5 of 5
Pages: 12345