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Re: How can I get percentile values of a dataset? - 3 years ago

Hi, Xiaodan- Sounds like you might want to use 3dBrickstat: with the following option: -percentile p0 ps p1 write the percentile values starting at p0% and ending at p1% at a step of ps% Output is of the form p% value p% value ... Percentile values are output first. Only one sub-brick is accepted as input with this option.

by ptaylor - AFNI Message Board

Re: 3dClusterize -> Fatal Signal 11 (SIGSEGV) received -> mri_maskify ; AFNI_18.2.15 - 3 years ago

Hmm, I think there should be a data set entered after the "-pref_map ..." option, for one thing. Also, there is no option called "-savemask". I think that should be deleted? Do either/both of those fix the crash? --pt

by ptaylor - AFNI Message Board

Re: 3dNetCorr '-push_thru_many_zeros' not working - 3 years ago

Does your mask include lots of voxels with null time series (or *any* of them)? I would have thought if it doesn't, then it should work. If it *does*.... well, I don't think it should, esp. for this context. (I'm on vacation/traveling at the moment, so I can't set down and run a lot of tests easily.) --pt

by ptaylor - AFNI Message Board

Re: 3dNetCorr '-push_thru_many_zeros' not working - 3 years ago

Do you have ROIs of *all* zero time series? If so, the help description for "-push_thru_many_zeros" notes that it won't push through that situation. -push_thru_many_zeros :by default, this program will grind to a halt and refuse to calculate if any ROI contains >10 percent of voxels with null times series

by ptaylor - AFNI Message Board

Re: Error in affine step - 3 years ago

Hi, Tamara- Thanks very much for posting those details-- I do see what the problem is right now. I think it is extremely subtle. I think it has to do with the fact that the outputs of @SSwarper in this case have a funny name ending with multiple volumetric file extensions: instead of being just ".nii.gz" or ".nii", they are ".nii.gz.nii". afni_proc.py ca

by ptaylor - AFNI Message Board

Re: The confusing output of orientation from 3dinfo - 3 years ago

Hi, Peng Ren- This is the orientation information: 3dinfo -orient FILE ... which in your file's case is RPI. The part of the header describing/showing this orientation information is: first (x) = Right-to-Left second (y) = Posterior-to-Anterior third (z) = Inferior-to-Superior [-orient RPI] You can change the orientation with something like 3dresample -orient AIL -prefix NE

by ptaylor - AFNI Message Board

Re: Error in affine step - 3 years ago

Hi, Tamara- Could you please paste the full output of the errors that afni_proc.py is giving you? Please also paste what is returned by: afni -ver Without these outputs, it will be impossible to know what afni_proc.py is having troubles with. If @SSwarper has run, then its outputs should be usable by afni_proc.py fine. Another sidenote for future reference: @SSwarper's syn

by ptaylor - AFNI Message Board

Re: Error in affine step - 3 years ago

Hi, Tamara- It would be useful to have the exact, copy+pasted error message you are receiving, actually. @SSwarper outputs *.nii files (and aff12.1D files), and I have used its results fine in afni_proc.py previously, so I don't think that naming should be a problem. Some notes on that afni_proc.py command: First, a sidenote: Probably it would be preferable to use MIN_OUTLIERS a

by ptaylor - AFNI Message Board

Re: Error in affine step - 3 years ago

Hi, Tamara- I think I have run into that error due to the ordering of the blocks when using -volreg_tlrc_warp. What is your full afni_proc.py command? Here is just the @SSwarper and the alignment parts of an afni_proc.py script I had run-- note the order of "align tlrc volreg" blocks with the present flags. \mkdir -p $owarp @SSwarper \ -input $anat

by ptaylor - AFNI Message Board

Re: Skull Stripping - 3 years ago

Hi, Tamara- Yep, those visual QC steps all look good. From the point of view of checking how the nonlinear alignment aspect worked, you would also want to check that the sulcal+gyral patterns between the olay and ulay line up, as well as things like tissue boundaries. (Note that in the medial-sagittal slices, like where the slice=1L, one can indeed expect to see "sheets" of outli

by ptaylor - AFNI Message Board

Re: DTI Analysis in AFNI - 3 years ago

Hi, Kelly- << Does anyone have experience running DTI analysis in AFNI? >> --> Yes. There is a fair amount of step-by-step documentation here, with commands/scripts: Some of the lectures+PDFs here might be useful: And finally, some more help on specific programs in AFNI: << Species: pig! >> --> No. (Or, more accurately, I don't...) I w

by ptaylor - AFNI Message Board

Re: Masks - 3 years ago

Actually, I see that I made a mistake in my previous code listing: I forgot to *use* the mask MMM.nii.gz that was created in the 2nd command in the third command... whoops! This is what should have been written initially (and I will edit my previous answer to be correct and match this, so that future generations are not thrown off by my error): # concatenate data sets of interest 3dTcat -

by ptaylor - AFNI Message Board

Re: Skull Stripping - 3 years ago

Hi, Tamara- I hear ya on not wanting to reprocess. My thought process is: it really *shouldn't* matter about mixing different processing results, as long as all the brains are skull-stripped well. However, it might be possible that one method skullstrips one region with consistent differences than another, and then there are systematic alignment differences for some subjects, and that

by ptaylor - AFNI Message Board

Re: Skull Stripping - 3 years ago

Hi, Tamara- The two templates *do* have different per voxel values, even though they appear to overlay pretty much exactly. The "3dinfo -history" of each file tells a bit of their respective stories. For MNI152_T1_2009c, its history is one primarily of scaling: 3dcalc -a mni_icbm152_t1_tal_nlin_asym_09c.nii -b mni_icbm152_t1_tal_nlin_asym_09c_mask.nii -expr 'a*step(b)*255

by ptaylor - AFNI Message Board

Re: Installation error - 3 years ago

Hi- We haven't put up official install instructions for Ubuntu 18.04 yet, but several people have chipped in advice, including this recent one: Please give that a go and see if that solves the issues. Thanks, pt

by ptaylor - AFNI Message Board

Re: Skull Stripping - 3 years ago

I would try using @SSwarper ("skullstrip + warp") before running afni_proc.py: It will both skullstrip the anatomical *and* calculate a nonlinear warp to template space (using 3dQwarp). Target data sets for it include things in the distribution that end with "_SSW.nii.gz", as described in the @SSwarper help file; if you are using one of those as target template spac

by ptaylor - AFNI Message Board

Re: Masks - 3 years ago

Hi, Emily- I will assume that each "mask" file actually still has the probability value in it-- that isn't just a binary map. First, you can provide the set of files to 3dTcat to make a single, 4D data set. Then, use 3dTstat to make a mask where there are nonzero voxels at any point across time; finally, provide the concatenated dataset and mask to 3dTstat, and have it make

by ptaylor - AFNI Message Board

Re: AFNI for Ubunutu 18.04 - 3 years ago

Hi, Kiyotaka-- Great, thanks. At some point in the near future we will finalize build instructions, likely incorporating this-- thanks for sorting this out. --pt

by ptaylor - AFNI Message Board

Re: Problem with installation - 3 years ago

Hi- We haven't put up official install instructions for Ubuntu 18.04 yet, but several people have chipped in advice, including this recent one: Please give that a go and see if that solves the R issues. Thanks, pt

by ptaylor - AFNI Message Board

Re: AFNI installation problem - 3 years ago

Following some steps from here that may have been updated since you were installing: ... can you run this: cd curl -O tcsh @update.afni.binaries -defaults -package macosx_10.7_local which will take care of a lot of the library errors you are seeing. Then you should be able to run sudo rPkgsInstall -pkgs ALL more easily to install the R packages. Let us know how that goes.

by ptaylor - AFNI Message Board

Re: 1dDW_Grad_o_Mat++ and DIFFPREP - 3 years ago

Hi, Bit-Warrior- Lots of things to unpack here. 1) OK, I will address some features of DIFFPREP, but just usage. From their help file: --dwi Full path to the DWI NIFTI image to be corrected. Only provide this if a LISTFILE is not provided. Bmatrix and phase parameters also need to be entered. --bvecs Full path to the Bvecs file. Only provid

by ptaylor - AFNI Message Board

Re: 1dDW_Grad_o_Mat++ and DIFFPREP - 3 years ago

Hi, Bit-Warrior- (DIFFPREP questions will have to go to the TORTOISE folks. I will just note that it is possible in v3.1.1 and onward to dwi/bvecs/bvals files directly into it, using option flags of those names.) Can I please have some more details of what you are trying to do and precisely what isn't working? 1dDW_Grad_o_Mat++ can have many types of bvec/grad/bmatrix and bval. Th

by ptaylor - AFNI Message Board

Re: 1d_tool.py: no "-csim_show_clustsize" option (ERROR): Ubuntu 14.04, AFNI Precompiled binary Debian-x86_64-1-gnu: Jan 23 2018 - 3 years ago

Hi- That version is old enough that I am not sure that it would have the option in question. The most recent build version of AFNI, with accompanying binaries, is from less than a week ago. How are you getting your AFNI binaries? Is it through Neurodebian, for example? If that is the case, that version has often been several months behind the most recent one distributed by AFNI. We

by ptaylor - AFNI Message Board

Re: FATCAT: Missing files 3dTrackID - 3 years ago

Yep, that's normal. See, for example, from pg 32 onward here describing more about the *.grid files: But, all the targets in a network are not necessarily connected directly to all other targets (that is the case biologically, and also for tracking, possible for related or different reasons); in general (and esp. for larger networks), that is not the case, and the "zeros" in t

by ptaylor - AFNI Message Board

Re: FATCAT: Missing files 3dTrackID - 3 years ago

Hi, Sondos- I think that isn't an error or anything, but a sign that there was no direct connection found between ROI1 and ROI2; there were apparently connections found between pretty much all of the other possible pairs in that case (a large amount of interconnectedness which I haven't really seen before, but can be OK in principle). If you look at the *.grid files, my guess is

by ptaylor - AFNI Message Board

Re: FATCAT: Probabilistic tractography acting up? - 3 years ago

Hi, Sondos- Output text files of properties are "*.grid" files; please search for "grid" in the 3dTrackID help file for more information, and also in this online documentation for more description: For more information on the tracking functions and how they work, please see this documentation: For probabilistic tracking "WM ROIs" or "WM connections (

by ptaylor - AFNI Message Board

Re: 3dTrackID - 3 years ago

Well, the fat_proc_connec_vis program is designed to read in multiple data sets after "-in_rois ..", each assumed to be a mask/map of a single ROI. It then turns each of those into a separate surface file ("*.gii"), and then those can be viewed together with SUMA. (Supplementarily, it also makes+applies labels from each file name.) You have a good idea to try to load in t

by ptaylor - AFNI Message Board

Re: 3dTrackID - 3 years ago

What command are you using to visualize the files? And are you trying to look at the network of ROIs, or at the output of tracking? --pt

by ptaylor - AFNI Message Board

Re: On concatenating resting runs - 3 years ago

Hi, Gustavo-- Well, if you are running out of degrees of freedom/time points in each time series without even bandpassing, then it seems like these subjects should probably not be used-- there is just too much motion, presumably. --pt

by ptaylor - AFNI Message Board

Re: suma libGLU.so.1 issue - 3 years ago

... and I see that part of the confusion might be due to the fact that we didn't list the CentOS-specific binaries for the CentOS builds in the instructions. That has now been fixed and should be visible here: (basically just running @update.afni.binaries for the correct package specification, which Rick noted in a separate reply here). --pt

by ptaylor - AFNI Message Board