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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
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Pages: 12
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Sorry just saw this.
I apologize but I need clarification. I am not sure how to check where my compiler (and am not sure what is meant by "the path to the clang that is being applied") is coming from. I would assume from brew tree, as I had brew and not conda I believe. Although I have since installed conda last week.
Thanks!
Current output of afni check is:
----------------
by
kxd344
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AFNI Message Board
Hello, I tried both of those things and then tried installing afex again, but still errors everywhere :/. I can send error logs if it helps. Thanks!
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kxd344
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AFNI Message Board
I cannot get the afex R package to install. Among some other issues with installation that I am stuck at.
I tried the following:
(1) setting LD_LIBRARY_PATH = /usr/local/lib in my .zshrc, hopefully that is the right path
(2) brew install gcc
(3) Installing afex package in R with install.packages('afex')
-- this was giving errors like "ld: library not found for -lgfortran&quo
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kxd344
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AFNI Message Board
Hello. I know my slice timing should be siemens style -- so with an even number of 32 slices like this: [2:2:32 1:2:31]. However, the way this was done in the scanner, the NIFTI files do not have this specific information, so when I use dcm2niix the json files do not have correct record of the slice timing (rather, it refers to some variable that I assume outputs the correct numbers).
I am att
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kxd344
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AFNI Message Board
When I did 11b in the past, I still did SSWarper first, and just then used that (and anat has no skull). Basically I made 11b just like 11, except for anything having to do with the ventricle mask creation type stuff.
All this being said, you are correct that whether it is pythonic or not does not make a difference as I just tried it with basic again and I did not get the correct files in inde
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kxd344
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AFNI Message Board
Thank you! This is all very helpful!
Interestingly, I think I figured out this may be related to a slower internet connection. I have my files auto-update/sync to a secure network. It has never given me issues before, but I realized that the day I was running into this issue my ethernet was not working and instead I was on WiFi. As soon as I moved my files to a different local directory that d
by
kxd344
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AFNI Message Board
I had the same issue with no alignment (ve2a and va2t) output for example 11. However, I used to do example 11b and I would get the alignment output. The only difference I can currently guess with comes with the html style. 11b does not differ from the default (basic) whereas example 11 has it set to pythonic. Perhaps the pythonic version misses including ve2a and va2t? I am rerunning example 11
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kxd344
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AFNI Message Board
Hello, I am using afni_proc.py to generate a resting preprocessing data script (11b). I have done this in the past, including on the data I am currently examining through the same computer, without issues (even over the past few days). However, today when running the generated script, I run into the error "attributeError: 'NoneType' object has no attribute 'input'" w
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kxd344
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AFNI Message Board
Thank you. I guess I don't quite follow "time series has zero mean" or how to check that. It is residuals from resting state processing.
I will look into finding the weight vector in the results directory. We did use afni_proc.py for this.
Thanks!
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kxd344
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AFNI Message Board
I am running analysis of preprocessed rs-fMRI data, want to measure correlations between the Glasser ROIs (then use these as inputs for classification analysis).
I am using 3dNetCorr, with inset of errts.SUBJECT.fanaticor_tlrc, and in_rois with the Glasser atlas (but resampled to same grid as the errts).
I want to make sure I am not making a large error - so 2 questions:
(1) I decided to
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kxd344
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AFNI Message Board
Hello,
I tried what you suggested, but I am still getting the same Fatal Signal Errors which stops SSwarper from working. I have confirmed that the OpenMP thread count was reduced to 4.
+++ Command Echo:
3dQwarp -lite -base /Volumes/Research_Data/Rhoades_Projects/RestingStatefMRI/Masks_Templates/MNI152_2009_template_SSW.nii.gz[0] -source Sub_037_01_anat_warped/junk.SSwarper.PUsdWbXzVb
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kxd344
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AFNI Message Board
Thank you very much for all the help, I will give that a try now.
There is only 1 other issue I am getting for a few subjects:
3dAllineate -base final_epi_vr_base_min_outlier+tlrc -allcostX -input anat_final.Sub_016_01.11b.SSwarper.rest+tlrc
tee out.allcostX.txt
++ 3dAllineate: AFNI version=AFNI_20.1.14 (Jun 10 2020) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./a
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kxd344
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AFNI Message Board
OK, thank you. I tried setting OMP_NUM_THREADS to 4 with
set OMP_NUM_THREADS = 4
in my script. When I run @SSwarper, it still gives the output of
Default OMP_NUM_THREADS is 20
Do I need to set it differently?
After several passes of this script, I am finally down to one last subject with this issue, but this issue keeps happening to them regardless.
++ 3dQwarp: replacing source data
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kxd344
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AFNI Message Board
Thanks for doing that. It is odd. The mac I am using (I remote serve into my lab's Mac with TeamViewer) has 64GB ram I think, or at least 32GB. OMP_NUM_THREADS=20 is what showed... it worked throughout most of yesterday, and then of course, after I stopped watching it last night, it errored out with the same type errors on later subjects. To me then, this seems like some sort of bizarre issu
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kxd344
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AFNI Message Board
Thank you very much! I don't believe I have -giant_move in mine, but it's quite possible that for the subjects where it didn't work, perhaps they are ones that require -giant_move. I will give that a try.
Thanks again.
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kxd344
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AFNI Message Board
Absolutely. I uploaded the script I ran as a .txt in my files -- Create_Run_Preprocess_Script_11b_SSwarp -- (I assume/hope you have access to that?). The script is roughly running example 11b from afni_proc.py to process my resting state data with my anatomical but I have it running @SSwarper first to skull strip and put in MNI space and then using those warp files for the afni_proc.py.
The re
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kxd344
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AFNI Message Board
Sure, thank you. I uploaded it (KeithDodd.tgz), and I included the anatomy and resting state files for one of the subjects where I am getting the error (same one we have been discussing). Thanks again!
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kxd344
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AFNI Message Board
Sure, assuming I understand correctly that the dset is the same as my input data set to @SSwarper:
3dinfo -o3 Sub_004_01_anat+orig.
-118.359001 -161.014999 -70.319000
3dCM Sub_004_01_anat+orig.
2.58212 -33.4768 0.161026
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kxd344
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AFNI Message Board
When running @SSwarper, I am often getting errors with it, similar to this one I have pasted below. Oddly, it works for some of my subject data, but fails like this for others. I cannot attach my .afni.crashlog as it is not an image, but I have also pasted some of what it displays at the bottom of this.
Please let me know if you need more information.
Thanks!
+++ Command Echo:
3d
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kxd344
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AFNI Message Board
I am getting very similar issues (and only with some of my subjects), do you remember what fixed it for you?
Thanks!
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kxd344
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AFNI Message Board
Thank you! That is helpful. As a side question, if I make a post, but then figure it out later, is there a way for me to close the discussion or delete my post? I don't mean to keep throwing too many questions at you all, especially if I manage to work it out later. So far, I have only found a way to edit posts, but not delete or "close."
Thanks,
Keith
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kxd344
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AFNI Message Board
PyQt4 seems to be no longer downloadable in Ubuntu 20.04 which does not allow uber_proc.py to be used. I've been trying to find workarounds to installing PyQt4 or using uber_proc.py, but so far failing. Is there a work-around that I am missing?
Thank you!
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kxd344
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AFNI Message Board
Hello,
Goal(s): I am trying to process resting state dicoms with afni_proc.py (specifically example 11), but am having trouble figuring out how to get it going.
What I have: For each subject i have Dicoms of both resting state data, and of T1 data.
Computer: Ubuntu 20.04
What I have tried:
(1) dcm_2niix_afni (to convert files to NIFTI)
-- unsure what to do after that (or if that is
by
kxd344
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AFNI Message Board
Hello, I realized my other thread was based on Ubuntu 20.04 and I finally got that one to seemingly work thanks to your help. I am still having issues on my MacOS. I ended up uninstalling everything, and following the directions from another thread here with MacOS 10.15 (Uninstalled anything with afni under root, reinstalled under my user account, and installed R 3.6.3 since 3.6 is supposed to be
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kxd344
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AFNI Message Board
Thank you. Using the -curl option got me further. Here is the output for the MacOS now with -checkall. There are still several failures it seems.
One thing I am especially confused about is "consider setting DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace" as I have confirmed with echo $DYLD_LIBRARY_PATH that it is set to that (and there is an export line in my .bashrc that is alrea
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kxd344
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AFNI Message Board
Thank you.
I ran that on my Ubuntu computer and it appears to be up to date there.
On my MacOS 10.15 however, I get errors when I attempt that update as stated. At first I ran it without sudo privileges and it told me
** you do not have write permissions in the install directory
(install dir = /Users/nameofusersubstitutedhere/abin)
So I decided to run it with sudo, but that still gav
by
kxd344
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AFNI Message Board
Sorry, I also had to install AFNI on MacOS version 10.15.4 and I ran into some similar issues too. I used this page. Here is the output of the check stage:
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 19.4.0
version: Darwin Kernel Version 19.4.0: Wed Mar 4 22:28:40
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kxd344
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AFNI Message Board
Thank you that was helpful, I am closer. I still have a few issues.
First, what I have done since my last post:
(1) I ran the lines you stated.
(2) I installed Miniconda for python 2.7 (I already had for python3 installed). I have confirmed that both python3 and python2 work, although it seems like python3 is the default if I just type "python" into my terminal.
(3) I installed R
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kxd344
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AFNI Message Board
OK, I stepped through step 2 again bit by bit and I uncovered some of the issues (although I am still unsure how to fix):
Lines that do not work include:
sudo apt-get install -y xfonts-base python-qt4
sudo apt-get install -y python-matplotlib
sudo apt-get install -y libssl-dev libgfortran3
The rest seem to have worked once I went line by line. suma -update_env is now working. I realize
by
kxd344
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AFNI Message Board
I am trying to install AFNI on Ubuntu 20.04 LTS. I followed all instructions found here. I was getting some warnings/errors throughout, for example with libxm4 (libXm.so.4) not being installed -- which that alone seems to lead to major errors (e.g. suma -update_env won't work, AFNI won't open, etc.). I have a .txt. file with the output from afni_system_check.py that I can email, but I h
by
kxd344
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AFNI Message Board
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