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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
Results 151 - 180 of 2305
Hi, Robin-
That EPI has a fair amount of brightness inhomogeneity. See how a lot of sulcal/gyral structures appear washed out and hard to see by the brightness around the edge.
To help deal with that, we created a new local unifizer that seems to really help with EPI-anatomical alignment of human FMRI datasets (*animal datasets have more external features, so still working on some special
by
ptaylor
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AFNI Message Board
Hi, Giuseppe-
Indeed, the order of points in the text file matters---they would have to be given in the order you want the line segments to be drawn.
To be clear, this is a veeery primitive algorithm for doing this... Maybe there is a cleverer way, the way that shapes could be made is so general, it is pretty tricky.
I think using the draw dataset plugin might be the best way to accom
by
ptaylor
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AFNI Message Board
Just to note: in looking at the data, the contrast was a bit different than what might be expected; using the "nmi" cost function seems to sort out the EPI-anatomical alignment. So, changing:
-align_opts_aea -cost lpc+ZZ -check_flip \
to
-align_opts_aea -cost nmi -check_flip \
In most cases, starting with "lpc+ZZ" would still be recommended; but then there are altern
by
ptaylor
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AFNI Message Board
Hi, Brady-
Re. 1) You can run:
3dinfo -ad3 DATASET
... to see the voxelsize. Also, you might check:
3dinfo -n4 DATASET
... to see the dimensions (3 spatial, 1 temporal). Perhaps just:
3dinfo DATASET
would be useful, to view lots of the header info/properties.
Re. 4) That takeaway sounds reasonable, as a general rule of thumb. I would always try to look at the output mask and se
by
ptaylor
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AFNI Message Board
... and I notice now that the infilling did a bit more than desired, based on relatively convexity... Have to ponder about that.
--pt
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ptaylor
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AFNI Message Board
Well, OK. If your points are all in a single plane, as in that image, here is a script to connect successive points (defined as a 3-column text file of XYZ locations, and the first line should be repeated as the last, so that the shape gets closed.
I used the following file as the "points.txt" below:
-6.2 6.2 43.8
6.2 6.2 43.8
16.2 6.2 41.2
23.8 6.2
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ptaylor
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AFNI Message Board
Hi, Brady-
OK, understood about the hardware constraints.
Re. 1) Wow, that is a huge number of voxels in the mask! Can I ask what spatial resolution the output data has? For a 2.5 mm isotopic EPI output dataset in the Bootcamp example, there are only 68,809 voxels. So, are your output voxels around 0.75mm isotropic or so?
-> and sorry to hear your computer got bored with AFNI running
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ptaylor
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AFNI Message Board
Hi, Maya-
Well, you could just keep listing each region you *don't* want to have in that comma-separated list within the angle bracket. The benefit of that is you can clearly check and doublecheck your list.
Though, I think that the FreeSurfer ROI labelling might help this. If I am not mistaken, the numbering 1-255 within both of their default parcellations covers the non-cortex and
by
ptaylor
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AFNI Message Board
Hi, Maya-
There are a couple ways to get this info.
To see the labeltable in an ROI file that has them (and those *REN* files have 'em), you can run:
3dinfo -labeltable aparc.a2009s+aseg_REN_gmrois.nii.gz
In your AFNI binaries directory, you can also see the files used to create those labels, which are called:
afni_fs_aparc+aseg_2000.txt
afni_fs_aparc+aseg_2009.txt
The numbers
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ptaylor
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AFNI Message Board
Hi, Brady-
A couple of sidenotes to start, which I hope might be useful (apologies if they aren't!):
From this recent paper:
... there is github code for several processing examples of various AFNI commands:
... which might be useful. In particular, the use of permutations for clustersize estimation with 3dClustsim in 3dttest++ that was described here (see Fig 5):
https://pubme
by
ptaylor
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AFNI Message Board
OK, looking at the data, the reason that PC calculations run into trouble---note that this runtime warning appears as another sign of it:
*+ WARNING: Badness in partial correlation calculation.
Normalizing factor is <=0 (how to take sqrt?)!
-> making all zeros.
---is that the number of ROIs in the "-inset ." is greater than the number of time points in the input data; this
by
ptaylor
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AFNI Message Board
OK, thanks for sharing that.
Some of the errors in the "please fix" can be ignored at the moment (e.g., the stats program ones, because on a Mac at the moment users are required to use R v3.6.*).
Installing matplotlib would greatly improve the APQC HTML, because all the line plots will look a lot nicer (and a few other things get calculated).
From these two messages:
* c
by
ptaylor
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AFNI Message Board
I don't think a command line program could do this generally.
As you mention, though, this is doable in the plugin.
I'm curious where the points came from? Is there some other step in their creation that could be used to help this goal, perhaps?
--pt
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ptaylor
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AFNI Message Board
Hi, Dante-
OK, I will email you offline about the data. I am puzzled that PC would be uniformly zero while the standard correlation isn't.
--pt
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ptaylor
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AFNI Message Board
Hi-
That command produced an image for me (using a different anatomical dset that I had).
Can you please provide the output of
afni_system_check.py -check_all
?
thanks,
pt
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ptaylor
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AFNI Message Board
Hi, Dante-
Well, with my test data here, PC and PCB are not full of zeros, even when using either '-weight_* ..' option. I might have to get your data to see about that?
I also don't know about using the partial correlation ("PC") matrix with the 3dMVM- or 3dMLE-based approach as the next step. Those are using the set of correlation values for comparisons altogeth
by
ptaylor
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AFNI Message Board
That is a topic near-and-dear to our collective hearts.
You can use @chauffeur_afni to "drive" automatic image/montage creation. Examples are provided here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/auto_image/auto_%40chauffeur_afni.html
This can be combined with 2dcat, too:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/auto_image/auto_2dcat.html
Im
by
ptaylor
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AFNI Message Board
Hi-
If I could make a few comments---
+ I notice you explicitly ask for the "basic" form of QC HTML:
-html_review_style basic \
The "pythonic" one is more complete and nicer-looking, and only adds the requirement of having Python's Matplotlib module (ver >=2.2.3) installed. That might provide a nicer QC experience?
+ You have nonlinear alignment to a templa
by
ptaylor
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AFNI Message Board
Howdy-
I think there is bad header information in that dset, which defines what plane has what interpretation.
It is possible to just re-set (or "refit") the header information, but it would be good to know how this came about. Where did this dataset originate, and what conversion/processing steps have been performed on it?
--pt
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ptaylor
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AFNI Message Board
Hi-
I believe the count of TRs per stim is from the convolved time series, which do appear to overlap a fair amount.
Note that the afni_proc.py QC (APQC) HTML does calculate the number of censored time points per stim, even providing some warning levels. Have you looked at that? There should be a QC_${subj} directory in your AP results output, and you can open the index.html file there.
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ptaylor
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AFNI Message Board
... and after last night's build, AFNI ver 22.3.05 contains this discussed update. It should already be on Biowulf, and/or you can "@update.afni.binaries -d" your local OS to update the binaries there.
Please let us know how that looks.
--pt
by
ptaylor
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AFNI Message Board
Okeydoke. I assumed you would opt for that, so I have put that into the code base, and we will aim to do a build this evening with it, so it will be available tomorrow. Your option of interest will be:
-weight_corr WCORR :input a 1D file WTS of weights that will be applied
to estimate a weighted Pearson Correlation. This
is different than the
by
ptaylor
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AFNI Message Board
Hi, Dante-
Ooook, I think this can happen when the time series is not already demeaned before entering it into 3dNetCorr. If a residual time series is entered, which should have a mean of zero, then this large change would not happen. If you have a time series with a mean far away from zero, and then apply a weight that is zero in some places, that will look like a giant spike in the time se
by
ptaylor
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AFNI Message Board
OK. There are a couple "attributes" to add to the dset to attach the statistical information for the p-to-t calcs. These can be aded in a couple different ways, this (below) seems the easier one than putting in individual attributes.
Let's say you have a dset of 2 subbricks, where the [0]th brick is an effect estimate, and the [1]th brick is a t-stat with 412 degrees of freedo
by
ptaylor
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AFNI Message Board
Howdy-
Just to note, the magic of internal t-to-p (and vice versa) calculations is not limited to BRIK/HEAD datasets; NIFTI datasets can have this happen, as well.
AFNI statistics program populate AFNI header fields that contain degree-of-freedom (and other stats label) information, and that is what is used. These include BRICK_STATAUX and BRICK_STATSYM. The FDR curve is created in a simi
by
ptaylor
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AFNI Message Board
Hi, Dante-
Like Antaeus of old, run-ins with hideous details just (counterintuitively, perhaps) make AFNI programs stronger!
I ran your commands with different data (the FATCAT_DEMO data), using a weights file of all ones, and things went fine---the correlation values were unchanged from the original. So I wonder if the issue you are seeing is particular to that data in particular---what d
by
ptaylor
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AFNI Message Board
Hi, Sebastien-
Yes: start the GUI, and arrange it as you want.
Then click on "Define Datamode" (in the 2nd column of the GUI, middle-ish). Then in the menu that opens, click on Misc in the bottom row. Then click on "Save Layout"---I usually then just hit Set select the default file name ".afni.startup_script", and a file of that name will reside in your direc
by
ptaylor
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AFNI Message Board
How about the following? It uses integer division, so you have to decide how you want to round things.
#!/bin/tcsh
set dset_roi = THE_DATASET_NAME
# get the 6 extents in terms of IJK slice indices
set extent = `3dAutobox -extent_ijk "${dset_roi}"`
# select out the min/max along the AP axis
set apmin = ${extent[3]}
set apmax = ${extent[4]}
set div1 = `echo "scal
by
ptaylor
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AFNI Message Board
If the colors are too dazzling, you can lower the opacity of them---that is one reason they might be bright to start with, so they can take some opacity reduction to show structure underneath.
Happy to hear suggestions of "better" colorbars if you have some details of those, or if you could point to some example papers with such colorbars.
-pt
by
ptaylor
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AFNI Message Board