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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 1261 - 1290 of 2305
Hi, Giulia-
Just to make sure that your AFNI version is uptodate, what is the output of:
afni -ver
?
Thanks,
pt
by
ptaylor
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AFNI Message Board
I'm not sure what would be the problem. Python 2.7 is good.
I'll send you instructions for uploading the 5 subject (but not just single ROI) case, and take a look.
--pt
by
ptaylor
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AFNI Message Board
Hi, Jung-
For #1: I believe yes, the size of group and matrices are combining to make a large data table. You can see how many bytes it takes up with "ls -l ..." on the file name. 12 hours does surprise me a little bit, though.
For #2: I am not certain. My first thought would be that 3dMVM is running out of memory on your computer, but then there would have been a "kille
by
ptaylor
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AFNI Message Board
Hi, Patrick-
The "-Tsmooth KPB NITER" option to IsoSurface controls the smoothing/polishing of the created surface: KPB kind of controls the polishing strength (bigger is more agressive polishing) and NITER is the number of iterations. You can add more iterations, or increase KPB to make the output smoother.
I do think you'd have to re-run IsoSurface to do this. Here is a
by
ptaylor
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AFNI Message Board
Hi, Colm-
The dreaded "-weight_ts .." option now awaits you in 3dNetCorr. All you have to do is "@update.afni.binaries -d", and the power shall be yours.
Note that I think the correlation values will be pretty sensitive to this. In many ways, I don't think it is so much a weight as a scaling-- I don't think it just "emphasizes" more points than othe
by
ptaylor
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AFNI Message Board
Howdy, Colm-
Yep, that should be implementable in the next short while.
--pt
by
ptaylor
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AFNI Message Board
Hi-
The first one isn't a problem, it's just a note (we tend to write our scripts in tcsh syntax, so if you transfer snippets to the command line with variable names, it might not work; however, all AFNI commands themselves work in either shell fine).
For the second line, how about if you copy+paste this into a terminal:
echo "" >> ~/.bash_profile
echo "
by
ptaylor
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AFNI Message Board
Hi, Shankar-
Cool, good to know-- those run times seems consistent with the diminishing returns of extra threads per run after a while.
-pt
by
ptaylor
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AFNI Message Board
Hi, Shankar-
Cool, glad that is working well.
I think with multiple threading, there is a diminishing returns after a while: doubling the number of threads doesn't halve the runtime, because there is 1) some part of the processing that is not parallelized, and 2) there is computational cost to multithreading (organizing jobs, separating and rejoining data, etc.). Eventually, adding m
by
ptaylor
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AFNI Message Board
Hi, Shankar-
OK, cool, let's see how long that takes.
The reason that the extents might matter: the warping program at the heart of @SSwarper (the latter is actually a wrapper for a few AFNI programs, with 3dQwarp being the primary workhorse) has to make a grid encompassing both dsets on which to work; so, if the source and base dsets are veery far apart, then it has to make a big
by
ptaylor
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AFNI Message Board
Hi, again-
One more thought on this-- what is the output of:
3dinfo -extent DSET
... where DSET is your input to @SSwarper? If your data set has weird coordinates that aren't ~approx centered around (x,y,z) ~ (0,0,0), that could conceivably cause some issues, too, for speed/memory.
--pt
by
ptaylor
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AFNI Message Board
align_epi_anat.py is a wrapper for 3dAllineate.-- that is, when you run align_epi_anat.py, it actually just puts together a command with specific options present for 3dAllineate.
In the AFNI_history part of the 3dinfo output for a file, you can see both. Here is an example from the afni_proc.py Bootcamp example:
align_epi_anat.py -anat2epi -anat FT_anat_ns+orig -suffix _al_junk -epi vr_
by
ptaylor
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AFNI Message Board
Hi, Kirk-
What is your full output to "afni_system_check.py -check_all"? We don't know what kind of computer/OS/AFNI version/etc. you are using.
Also, are you running this remotely, or just on your local machine?
What is the output of this:
echo $DISPLAY
?
--pt
by
ptaylor
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AFNI Message Board
Hi-
Yes, you should update your version of R; I'm not sure why we link to that old one still, and I will update our instructions. This should be a modern enough version to use (3.5.3) on Macs:
(form the cran website, having 3.6.0 might require other installs to compile R libraries).
After updating your R, you should update your packages in the R, by running the following in the R
by
ptaylor
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AFNI Message Board
Hi, Shankar-
That seems excessively slow to me. I ran @SSwarper on a 1x1x1 mm**3 anatomical the other day using 5 CPUs and it took about an hour, I think.
Something to note-- that version of AFNI is veeery old, and there have been a lot of modifications to @SSwarper since then, as well as important ones to 3dQwarp. In particular, pretty recently Bob made the default 3dQwarp operation bo
by
ptaylor
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AFNI Message Board
Hi-
There is this column in the 3dClusterize tabular output:
Max Int : Maximum Intensity value for the volume cluster
... so the sign of that should tell you which cluster is pos/neg when using bi-sided (generally recommended) clustering.
In the GUI, when you hit the "Save Mask" button in the Clusterize Report controller, you will see the 3dClusterize command run on the co
by
ptaylor
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AFNI Message Board
Howdy-
You can add either of these options to suppress the commented text descriptions, and only output numbers (from the 3dClusterize help):
-nosum :Suppress printout of the totals
-quiet :Suppress all non-essential output
Note that even if you don't use the -quiet option, you can use 1dcat to dump the text from a file excluding the commented stuff-- this might
by
ptaylor
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AFNI Message Board
Hi-
That align_epi_anat.py command has commas, as well as a single apostrophe, in it-- are those just copy+paste features?
If the "itkxfm.1D" file is one made by ITK, then no, it will not work-- they use a different format for rotation description.
Would you be able to upload the data sets, and we can take a look? I will PM you instructions for doing so.
--pt
by
ptaylor
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AFNI Message Board
Hi, Ruyuan-
What commands have you tried so far, esp. in the Nudge+"align_epi_anat.py -pre_matrix ..." case?
--pt
by
ptaylor
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AFNI Message Board
Howdy-
That is odd. I am not sure; I just copy+pasted that command on my computer, and it worked for me.
A couple things:
1) what is your AFNI version? Output of: "afni -ver".
2) in that directory, what does the following show (don't know if it's possible that the files have bad permissions, for example?):
\ls -l *HEAD *BRIK* *nii*
?
--pt
by
ptaylor
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AFNI Message Board
Hi, Sam-
You input a non-bandpassed time series to 3dRSFC, and you can get out:
+ voxelwise map of ALFF (single value per voxel), which contains the sum of LFF amplitudes.
+ voxelwise map of fALFF (single value per voxel), which contains the ratio of LFF amplitudes to the full time series' amplitudes.
+ and similarly maps of RSFA and fRSFA, as well as a couple other related parameters.
by
ptaylor
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AFNI Message Board
Hi-
I don't think that the file after the "-1Dmatrix_apply" argument is correct. I ran your initial align_epi_anat.py command on my computer with BRIK/HEAD files, and the matrix didn't have the "+orig" part in that file name. Can you tell me what the output of this is?
\ls Q08.DLPFC.T1.Pre*_al_keep_mat.aff12.1D
I am assuming that it will be:
Q08.DLPFC
by
ptaylor
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AFNI Message Board
Cool, thanks. And what is the 3dAllineate command that is failing for you?
--pt
by
ptaylor
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AFNI Message Board
Hi-
What is your AFNI version ("afni -ver" output), and can you please copy+paste the command that you are using?
Also, it would probably be useful to know what command you used to generate:
Q08.DLPFC.T1.Pre+orig_al_keep_mat.aff12.1D
--pt
by
ptaylor
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AFNI Message Board
Hi, Sam-
For most RSFC parameters, one needs to specify a range of frequencies that define the "low frequence fluctuations" (LFFs) of interest. A typical range of LFFs in resting state might be approx. 0.01 - 0.1 Hz, for example.
fALFF is a ratio:
(the sum of amplitudes of those LFFs) / (sum of amplitudes of all frequencies in time series).
Bandpassing is the mechanism for se
by
ptaylor
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AFNI Message Board
The following posters from members of the AFNI group are being presented at OHBM, 2019:
Notizia dell'AFNI: Meet afni_proc.py–Your New Best Friend
Notizia dell'AFNI! AFNI now makes templates from your subjects easily!
Notizia dell'AFNI: Even easier FMRI QC, with afni_proc.py's automatic HTML review
Notizia dell’AFNI: Efficient Inter-Subject Correlation Analys
by
ptaylor
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AFNI Message Board
The source code has been rebuilt, so the fixed version should be available.
--pt
by
ptaylor
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AFNI Message Board
I have added a new option to 3dTrackID called "-trk_opp_orient":
-trk_opp_orient :If outputting *.trk files, you can choose to oppositize
the voxel_order parameter for the TRK file (only).
Thus, when inputting AFNI files with orient RAI, the
*.trk file would have voxel_order LPS; this is so that
f
by
ptaylor
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AFNI Message Board
Hm, I see. I am a bit stuck for ideas, then, unfortunately. We are teaching an AFNI Bootcamp this week and there is the OHBM conference next week, so I am away from any CentOS system to try anything else.
Looking online, it seems that R v3.6 is not available for CentOS yet, so updating the R version further won't be an option. I don't know if any other user with more experience
by
ptaylor
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AFNI Message Board