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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
As Paul said, the subcortical isn't included in the surface meshes. The general approach is to do each surface separately (left, right) and then a third analysis for sub-cortical. You could use 3dSurf2Vol to create a mask fo the whole-brain volume that isn't represented by the surface-based analyses.
-Peter
by
Peter Molfese
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AFNI Message Board
Look for the -blip_forward_dset and -blip_reverse_dset options in afni_proc.py. In this case, you'll need to do an analysis of the L-R data with the reverse blip (R-L) and then an afni_proc separately for the R-L data with reverse blip (L-R). The blip portion of the processing actually happens fairly early on, so you could modify the afni_proc output script to run the data through the firs
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Peter Molfese
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AFNI Message Board
The general recommendation around here is to use TORTOISE for all things diffusion, and you can see the updated instructions on the blog page you linked to for how to do the preprocessing. If there's something that TORTOISE doesn't do, a feature request could be made to add it.
More to your question: Vecwarp was written by Bob, and he's away at a Bootcamp for the next week.
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Peter Molfese
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AFNI Message Board
You should use auto_warp.py to normalize your T1 to MNI space. And then use 3dNwarpApply to apply that transform to your EPI data.
There is a new tool: @SSwarper that will take care of the skull stripping and nonlinear warping (via 3dQwarp) your T1 to MNI space, and then you can use 3dNwarpApply to apply the transformation to your EPI dataset. You'll see in the help, there are also ho
by
Peter Molfese
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AFNI Message Board
The "Clusterize" button can show you the significant clusters on the group maps. It's a combination of setting the correct p-value and looking for clusters of a particular size. The papers I mentioned above have more details.
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Peter Molfese
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AFNI Message Board
Hi-
Putting despike in blocks ends up running 3dDespike. Whereas the regress_censor_outliers simply removes them from the regression model. In some cases the latter is preferred, while in others both are recommended.
PM
by
Peter Molfese
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AFNI Message Board
Hello,
You might look at some of the educational resources. There are video recordings of recent bootcamps held at NIH.
The short answers are:
1. The p-value uncorrected isn't enough to get published (and for good reason). There are a few AFNI publications about responsible use of statistics that are relevant (1, 2).
2. Your options are to use FDR (q-values) or Cluster Corre
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Peter Molfese
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AFNI Message Board
Post your current afni_proc.py script and we can go from there.
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Peter Molfese
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AFNI Message Board
The best solution is to go back to the intermediate files and re-run the processing from there with the correct smoothing level. Filters are additive, so if you now applied a kernel of 4mm or 8mm, you'd end up with different values than you would have otherwise doing it in a single step.
One could make an argument of using 3dBlurToFWHM, but I would say go back and do it again. You cou
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Peter Molfese
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AFNI Message Board
Hi José,
We're still in the midst of writing the Haskins Pediatric Paper. You can checkout the poster here. But I'm happy to answer your questions about it.
-minpatch does go down to 5. But, as noted in the documentation, it's hard to optimize a search problem on that scale for multiple processors. I did play around with other options when making the Haskins Template, a
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Peter Molfese
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AFNI Message Board
Your 3dTshift warning about datasets already being aligned in time suggests that the slice timing information is not included in the dataset header (this is actually pretty common). You can specify a timing pattern using:
-tshift_opts_ts -tpattern alt+z
replace the alt+z with your actual slice time information
S L I C E N U M B E R
tpattern 0 1 2 3 4
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Peter Molfese
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AFNI Message Board
Lots of ways to do this... perhaps the easiest would be running the 3dcalc command on each of your masks to merge it with the reference, and then using 3dBrickStat with -positive option to figure out which one to keep.
for aMask in mask*+tlrc.HEAD
do
3dcalc -a ReferenceMask+tlrc.HEAD -b ${aMask} -prefix merged_${aMask} -expr 'ispositive(a)*ispositive(b)'
done
max=0
max_
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Peter Molfese
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AFNI Message Board
Hi Carole-
There's quite a few ways to do this... If you just want a count of the overlap, you should use 3dABoverlap. You could try something like this (bash syntax):
for aMask in mask*+tlrc.HEAD
do
3dABoverlap -no_automask ${aMask} Reference+tlrc
done
Once you have that working, you can use the -quiet option and pipe the output to a file.
-Peter
by
Peter Molfese
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AFNI Message Board
Against best advice... You could use 3dTcat in combination with (likely) 3dDetrend or some creative use of 3dSynthesize.
I might suggest that a (perhaps) slightly less evil approach would be to make your motion threshold more liberal (-regress_censor_motion).
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Peter Molfese
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AFNI Message Board
You can use 3dfractionize to downsample the ROI to your dataset.
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Peter Molfese
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AFNI Message Board
Hi Tamara-
That's a curious error message. Can you post your entire afni_proc.py command?
Also, it's worth updating your binaries for a variety of reasons. But one of the main ones is that we're currently recommending doing the nonlinear warp (and skull strip) outside of afni_proc.py using @SSwarper. An example usage is:
@SSwarper -input 9409.anat+orig -base MNI152
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Peter Molfese
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AFNI Message Board
Alt-z may not be appropriate. The best approach is to check with your scanner group or to read in the info using Dimon, which will output the slice information from the headers. You can then specify those timings into a file and use the @filename option of 3dTshift (or afni_proc.py).
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Peter Molfese
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AFNI Message Board
Hi Mariana-
You can use either 3dTcorr1D or 3dttest++ (or if you want to go super old school, 3dRegAna).
If you want to use 3dTcorr1D, you can follow instructions here.
If you'd prefer to use 3dttest++, then you can follow the instructions here.
The nuance of 3dttest++ is to then use 3dcalc to convert the t-value to a correlation via the t to R-square method.
3dcalc
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Peter Molfese
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AFNI Message Board
I'd start by combining all of the ROIs in such a way that you'll get a separate value for each one. You can follow some of the instructions laid out here. The key is to create a dummy (empty ROI) and then use 3dTcat to concatenate all of your ROIs together with the empty one first. You can then use 3Tstat with the -argmax argument, which will result in a single NIFTI (or HEAD/BRIK) t
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Peter Molfese
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AFNI Message Board
If you have a balanced design, you could use 3dANOVA2 or 3dANOVA3. If you have an unbalanced design or need to use covariates, you can use 3dMVM. Much of this is covered in the bootcamp documentation on group analysis.
-Peter
by
Peter Molfese
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AFNI Message Board
You could also try a modified afni_proc sequence that uses the previously preprocessed files. I wrote about this for comparing different basis functions, but you could just adapt it for different GLTs.
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Peter Molfese
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AFNI Message Board
I'll add that obliqueness will probably be solved with an alignment to an anatomical dataset. So I'd say that before you 3dWarp all of your data, perhaps look at the rest of your pipeline and decide if something down the road is going to handle it.
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Peter Molfese
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AFNI Message Board
Please post the output of:
afni_system_check.py -check_all
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Peter Molfese
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AFNI Message Board
Hello,
The errts.CON_EIU24.fanaticor+tlrc file is the "final" with ANATICOR processing. That's the file that I would focus resting state processing on.
-Peter
by
Peter Molfese
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AFNI Message Board
It may not have all of the features you need, but have you seen 3dStatClust?
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Peter Molfese
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AFNI Message Board
Hi rosaann-
There are a number of possible ways: You can try the Nudge plugin within AFNI's viewer. Alternatively, it's possible to use 3drotate.
-Peter
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Peter Molfese
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AFNI Message Board
Hi 2086,
You can do something like this:
3dROIstats -mask MyMask+tlrc.'<1>' MyDataset+tlrc.
Changing the 1 to other numbers can increment through. 3dROIstats will also output a column for each value in the dataset by default, which is my usual method. I then rename the columns (usually in R).
-Peter
by
Peter Molfese
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AFNI Message Board
You should remove the "mask" from your -blocks line. That should fix that error.
You may need to also remove the "-regress_est_blur_errts" which may also give an error.
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Peter Molfese
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AFNI Message Board
The debate is almost as old as (fMRI) time, with some people suggesting that you never regress out motion. But the AFNI way is to do both censor and regress out motion. Note that censoring means that those TRs don't contribute to the final stats, so the motion related to those TRs is also not considered.
I've played with motion censoring and regressors a decent amount, and while
by
Peter Molfese
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AFNI Message Board