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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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Results 31 - 60 of 145
Hi,
I'm contemplating using the blip_for and blip_rev options to afni_proc. However, before I dive in I'd like to get a better understanding of how to use them properly. From perusing the db_mod.py source code, it seems that each argument needs separate data sets. However, this prompts a couple of questions:
Should both of these two data sets be separate from the data sets provide
by
Colm Connolly
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AFNI Message Board
Are you missing a new line at the very end of the table?
by
Colm Connolly
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AFNI Message Board
You may have the OpenSSL library installed but you're clearly missing the openssl-dev package
try
sudo apt-get install openssl-dev
and then try tin install brms again.
by
Colm Connolly
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AFNI Message Board
From the sound of it you may need to install openssl and openssl-dev. Since you say you are using Ubuntu, you should be able to achieve this with
sudo apt-get install openssl openssl-dev
Note that openssl-dev and libcurl4-openssl-dev are not the same thing. the former is the development support part (e.g., the header files) of the library that provides SSL support. The latter iis the pat of
by
Colm Connolly
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AFNI Message Board
Hi,
Anybody got any idea how to have 3dttest++ pass athr and pthr arguments to 3dCustSim when 3dttest++ is run with the -Clustsim argument?
Thanks,
Colm.
by
Colm Connolly
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AFNI Message Board
Hi,
When running 3dttest++ with the -Clustsim argument, is there a way to have it pass the athr and pthr arguments to 3dClustSim rather than have it run with 3dClustSim with the default arguments? I'm specifically interested in begin able to pass -athr 0.01 and -pthr 0.008 to clustsim.
Thanks,
Colm.
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Colm Connolly
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AFNI Message Board
Thanks Daniel. I had completely forgotten about the 3dWarp option.
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Colm Connolly
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AFNI Message Board
Hi,
I have a whole slew of binary ROIs in MNI152 space @ 1mm resolution (182x218x182 voxels). Is there straightforward AFNI incantation to warp these from MNI152 space to match TT_icbm452+tlrc @ 4mm isotropic?
Usually I do this the other way around (TT->MNI) and use fsl to do the job. Now needing to go the opposite way I've realized I've no idea how to do this in AFNI
Any h
by
Colm Connolly
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AFNI Message Board
I may not have been clear enough so here's some sample bash code that does what I mean, I've put echo commands before the 3dZcutup, 3dTcat, and 3dDecon commands since I don't actually have any data with which to test this. Yo umay need to cut it up even more to get it to fit into memory depending on how many TRs you have, (which you didn't state).
#!/bin/bash
# 162 sli
by
Colm Connolly
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AFNI Message Board
You could also use 3dZcutup to break them into smaller blocks and run 3dDeconvolve on each of the blocks and then use 3dZcat to glue everything back together. However, I've not tried this.
by
Colm Connolly
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AFNI Message Board
Are your time series in a row or column? If I recall 3dfim+ likes the ideal file in a column. To convert from row to column is trivial, just add a ' at the end of your ideal file name on the 3dfim+ command line. Though you will more than likely need to add a \ before the ' in order to prevent the shell from interpreting it.
You command will look something like:
3dfim+ -input input+t
by
Colm Connolly
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AFNI Message Board
Hi everybody,
I'm trying to install AFNI for the first time in a very long time on my mac running 10.12.6. Looking in I see that there are several different binaries for MAC. I've downloaded (yesterday sept 27, 2017) the macos_10.12_local.tgz tarball and unpacked it. When I run afni -ver I get
When I try to tun it I get:
colmconn@Colms-MacBook-Pro:~/afni.macosx_10_12> ./afn
by
Colm Connolly
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AFNI Message Board
Hey,
Is 3dAutomask (generally) more generous in it's estimation of the brain when skullstripping EPI images than 3dSkullStrip?
I ask because in this screen shot (run on the same data from the same subject), on the left can be seen an invocation of align_epi_anat.py with 3dSkullStrip as the default and on the right is an invocation of aea with 3dAutomask as the skull stripper. Both in
by
Colm Connolly
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AFNI Message Board
Yep.
Attached is the whole csh script generated by afni_proc
I can provide the log file produced by this script as well if you'd like.
#!/bin/tcsh -xef
echo "auto-generated by afni_proc.py, Mon Apr 24 17:44:50 2017"
echo "(version 5.14, April 11, 2017)"
echo "execution started: `date`"
# execute via :
# tcsh -xef CMIT_01A.afniNeedlePreproces
by
Colm Connolly
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AFNI Message Board
Hey,
I'm trying to run an analysis script resulting from an afni_proc invocation (see below) but cat_matvec is crashing. Any idea what could be causing this problem?
I'm happy to upload the offending files if it would help.
This is using afni version Precompiled binary linux_openmp_64: Apr 12 2017 (Version AFNI_17.1.01).
afni_proc.py -subj_id CMIT_01A \
-s
by
Colm Connolly
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AFNI Message Board
Hey,
I've got a few questions about Gang's gPPI sample script.
Could the \' be added to the end of the 3dDetrend line to prevent it erroring out?
What is supposed to be in the one1.1D file and how should be it be created?
With respect to the line: waver -GAM -peak 1 -${TR} ${sub_TR} -input Inter_neu${cond}${cc}${sd}.1D -numout ${n_tp} > Inter_hrf${cond}${cc}${sd}.1D
by
Colm Connolly
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AFNI Message Board
Hi Brian,
Thanks for fixing this. However, the links are 404ing again this morning (PST). Can you please have a look again?
Thanks,
Colm.
by
Colm Connolly
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AFNI Message Board
Hi,
I'm trying to access the documentation at, for example, but am only getting 404 errors. Have these documents been moved somewhere else from where I might access them?
Thanks,
--
Colm.
by
Colm Connolly
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AFNI Message Board
have you tried @Align_Centers on the problematic subject's T1W and EPI images before trying to coregister them?
by
Colm Connolly
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AFNI Message Board
Hey,
I'm trying to align a lot of EPI data with poor contrast (there are no pre steady state volumes with sufficient T1 weighting to make using the LPC cost function by default viable for all subjects) with my T1 data.
To get a sense of what cost function provides the best alignment for a particular subject I'm running (from linux_openmp_64: Sep 4 2016 (Version AFNI_16.2.16)):
by
Colm Connolly
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AFNI Message Board
Yeah, I always have it set to reduce disk usage. Is the only way around it to unset it?
by
Colm Connolly
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AFNI Message Board
Thanks for the fix Rick. This now seems to work to a point. afni_proc will now generate a shell script but running it unmasks another error (all 3 of the pre-warped files exist):
afni_proc.py -subj_id 107_A -script 107_A.afniRsfcPreprocess.noanaticor.NL.csh -out_dir afniRsfcPreprocessed.noanaticor.NL -blocks despike tshift align tlrc volreg mask blur regress -copy_anat /data/sanDiego/machLe
by
Colm Connolly
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AFNI Message Board
Hi,
I'm trying to rerun some RSFC analysis and in doing so also trying to avoid rerunning nonlinear warping given how long it takes.
I'm running the following command from linux_openmp_64: Aug 19 2016 (Version AFNI_16.2.11)
afni_proc.py -subj_id 106_A -script \
106_A.afniRsfcPreprocess.noanaticor.N
by
Colm Connolly
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AFNI Message Board
I'm posting this on behalf of Fumiko Hoeft and Roeland Hancock @ UCSF. Please do not contact me about these positions.
==============================================================================================
Job Announcement, July 2016: Postdoctoral Fellow
Haskins Laboratories, 300 George Street, Suite 900, New Haven CT 06511
Qualified individuals are invited to apply for a f
by
Colm Connolly
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AFNI Message Board
I eventually got this to work, but I had to remove the tempdir argument to 3dttest++. However, I also had to ensure that AFNI_COMPRESSOR was not set as 3dClustSim could not read the -inset files if they were compressed. I got the following error:
3dClustSim -DAFNI_DONT_LOGFILE=YES -inset .//resid.CStemp.L_whole_amygdala.3mm.???.nii -prefix resid.CStemp.L_whole_amygdala.3mm.CSim -LOTS -b
by
Colm Connolly
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AFNI Message Board
Hi,
I'm experimenting with 3dttest++ to explore teh new resid and clustsim options but have run into a problem with it not working.
I'm running 3dttest++ as follows:
cd /data/sanDiego/rsfcGraphAnalysis/data//Group.results ; mkdir tmp.resid.clustsim.L_whole_amygdala.3mm ; 3dttest++ -resid new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid \
-CLUSTSIM \
-prefix_clustsim r
by
Colm Connolly
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AFNI Message Board
Hi,
I'm somehow managing to make AFNI crash, a feat I can, regrettably, repeat ad nauseam.
I'm loading in two sessions on the command line. The MNI brain found in the first session is loaded automatically by AFNI and then I load in a t test file as overlay. Next open new AFNI controller window and switch to the second session directory. Make the axial and sagittal views appear an
by
Colm Connolly
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AFNI Message Board
Page 2 of 5
Pages: 12345