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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: 123
Results 1 - 30 of 79
Hi,
Is there a surface-way, maybe by using the thickness map, to calculate the gray matter volume of a functionally defined surface ROI (in std.141 surf)? Or by using 3dSurf2Vol to map back to volume to calculate the gray matter volume? Is this as accurate as calculating on surface directly?
And does it make sense to compare the gray matter volume between two group, say young and old, unde
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EXP.2086
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AFNI Message Board
Hi Rick,
Is there a way to make `source("/usr/local/afni/AFNIio.R")` works in RStudio? It did work for R in terminal after add "R_LD_LIBRARY_PATH" in bashrc; but I could not make it work in RStudio. I tried to add lines below into ~/.Renviron file:
PATH=${PATH}:/usr/local/afni
DYLD_LIBRARY_PATH=/opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH=${R_HOME}/lib:
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AFNI Message Board
Hi Daniel,
Thanks for your reply. I tried as you said, and SUMA indeed opened with AbsThreshold off, but that for the brain (surface/spec/convexity) itself the AbsThreshold was off too, and the color of the brain became more white, which seemed strange. A drivesuma AbsThreshold switch for specific dset but not for all is more preferred.
Thanks,
2086
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AFNI Message Board
Hi Paul,
Thanks for your reply. I am sorry, it was my mistake! I used "3dBrickStat -positive -count" to show the ROI size, and it reported the sum size of several ROIs.
I used a A-B_#0_Coef brick of 3dDeconvolve result, restricted to same anatomical area between subjects first, as inset for 3dROIMaker to make constant sized GM ROI near the activation peak (-only_conn_top 500) whic
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AFNI Message Board
Hi,
I used these code to generate constant sized GM ROIs near the $fROI peak:
Quote
3dROIMaker -inset $fROI -thresh 0 -mask $wbmask \
-wm_skel $wmfa -skel_thr 0.2 -skel_stop_strict \
-only_conn_top 500 -inflate 1 \
-neigh_upto_vert -dump_no_labtab -nifti
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AFNI Message Board
Hi Paul,
Yes, you are right. When I post my answer I did not see your answer. 3dAutobox is much more faster than 3dmaskdump.
Thank you again,
2086
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AFNI Message Board
Hi Paul,
Thanks for your answer!
Yes, 3dAutobox is what I need!
Best,
2086
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AFNI Message Board
Hi,
How to get the location of the most posterior coronal slice location of a volume mask (1 in mask, 0 outside) ?
Thanks,
2086
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AFNI Message Board
Solution:
DO NOT use "-isorois+dsets" option, because SUMA will automatically loads the dsets (same name as gii) with the default color given by IsoSurface. Just solely output gii with "-isorois" option, then switch colormap in SUMA with drivesuma commands like this:
QuoteDriveSuma -npb $port -com surf_cont -view_surf_cont y -switch_surf rm.$ROI.k$ROID.gii -switch_cmap gre
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AFNI Message Board
Hi,
Is there a way to define the colors of IsoSurface dsets? There are three volume rois (val = 1/2/3), I want to apply the red/blue/green_monochrome colors to them, that will look better than the default colors given by IsoSurface. Or is it possible by drivesuma commands?
Thanks,
2086
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AFNI Message Board
Hi Paul,
Thanks for your detailed answer. I understand the role of having a uniform DTI reference now.
I was following the FATCAT tutorial, using the same axializing reference, and fat_proc_axialize_anat kept out data uniform, that's good. But when I tried to write this part in paper, I found I was not clear about this process. So could I write like this:
Quote We axialized our data
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AFNI Message Board
Hi Paul,
The FATCAT tutorial says that :
Quote
This takes the NIFTI T2w dset and axializes it with respect to the reference dset (here, from the MNI 2009 templates, which was manually AC-PC aligned and regridded ...
Is the MNI 2009 template not AC-PC aligned? Why re-AC-PC align it?
Is this understanding correct: it's a easy way (not need to manually assign anatomical markers) to auto
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AFNI Message Board
Hi Paul,
Thanks for your suggestions.
I think I did not fully understand the Local Pearson Correlation(LPC) score.
1. After keeping in the similar ROI (same surface std ROI mapped to volume) in different subjects:
a. Does the lpc value reflect the alignment at this ROI, and lager absolute lpc value means better alignment?
b. Does the lpc value at this ROI can be compared between subje
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AFNI Message Board
Hi Paul,
Thank you!
As we did analysis within same std.141 surface ROI for all subjects, then will it make sense to Surf2Vol the ROI mask for each subject, then calculate the lpc value within ROI masks on volume, then compare that value from different subjects? Is it too complicated for a supplemental analysis to show similar data preprocess? Or just show the overlay images of every subject
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AFNI Message Board
Hi,
Is it appropriate to compare the final lpc cost from different subjects/groups to show comparable data preprocess quality?
# record final registration costs
3dAllineate -base final_epi_vr_base_min_outlier+orig -allcostX \
-input anat_final.$subj+orig |& tee out.allcostX.txt
Thanks,
2086
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AFNI Message Board
Hi Rick,
Thank you. I understand, you don't have to explain it. I thought that post is too long, and the main problem has been solved, so I put it here.
Thanks,
2086
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AFNI Message Board
Hi Justin,
Thanks for your suggestion. I prefer the completion style in zsh more, actually.
Thanks,
2086
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AFNI Message Board
Hi Rick,
Thanks for your help. Yes, it works now except the 16 programs you mentioned above.
Thanks,
2086
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AFNI Message Board
Hi,
Quoteapsearch -update_all_afni_help provides auto-completion for bash and tcsh, how to modify that for zsh?
Thanks,
2086
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AFNI Message Board
Hi Rick,
It was the result after re-run: Quoteapsearch -update_all_afni_help
The problem seems to be that there is no program named "complete" in zsh, while there is in bash :
Quote
z@Z ~ % complete
zsh: command not found: complete
z@Z ~ % bash
The default interactive shell is now zsh.
To update your account to use zsh, please run `chsh -s /bin/zsh`.
For more details, pleas
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AFNI Message Board
Hi Justin,
All afni programs worked again, thank you very much.
The attribute was:
Quotecom.apple.quarantine
But there is still a small problem as with the zsh(default terminal in 10.15), when I open new terminal, it shows:
Quote
Last login: Wed Oct 30 10:04:10 on ttys001
/Users/z/.afni/help/all_progs.COMP.bash:1: command not found: complete
/Users/z/.afni/help/all_progs.COMP.bash:2:
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AFNI Message Board
Hi Rick,
Here the installation and afni_check log:
Quote
Last login: Mon Oct 28 23:24:06 on ttys000
z@Z tmp % tcsh -x ./@update.afni.binaries -local_package macos_10.12_local.tgz -do_extras
set prog = `basename $0`
basename ./@update.afni.binaries
set hostname = afni.nimh.nih.gov
set hostproto = https://
set hostsite =
set sysname = `uname -s`
uname -s
if ( 0 ) then
goto POST_HIS
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AFNI Message Board
Hi Peter,
Thanks for your reply and your suggestions.
And the result is that each lib called by AFNI needs to be allowed to run every time starting AFNI, and I haven't start AFNI successfully yet. Fortunately, it's not a computer for production.
2086
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AFNI Message Board
Hi,
AFNI is prevented to start on Mac OS 10.15.
Thanks,
2086
EDIT (rick): solved - see Justin's post and follow-ups
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AFNI Message Board
Moderator note: this question was originally asked on a separate thread. It is a separate question than that thread's discussion, and has been separated into a new thread for organizational purposes.
thanks,
pt
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Hi Rick,
Is there a way to only read AFNI brick labels without really read
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AFNI Message Board
Hi Rick,
Thanks for your reply. Yes, when sourcing from R. I use read.AFNI in R to do some data extraction, then do some calculation with R, and read.AFNI in R works more quickly than in Matlab. AFNI version before Jul 25 2019 works well, I did not test all versions after that, but version 22 Aug 2019 and version Aug 29 2019 showed the same error message.
Thank you,
2086
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