Show all posts by user
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
Page 1 of 2
Pages: 12
Results 1 - 30 of 46
sorry for chiming in
there's quite a bit already out there on suppressing background noise in MP2RAGEs to make skull-stripping work, e.g.:
-sam
by
storrisi
-
AFNI Message Board
hey all
any issues with AFNI and upgrading to the new XQuartz 2.8.3?
thx
by
storrisi
-
AFNI Message Board
hi AFNI gurus
most probably a dumb question but i ran fast ANATICOR and there's a volumized+tlrc volume in my .results.
i don't usually run fast ANATICOR so i believe this is the first time i'm seeing this output, which looks quite odd (see attached).
was this from the fast ANATICOR process?
i can't find evidence of its creation in the proc.* or in the volume's
by
storrisi
-
AFNI Message Board
hi Lysianne and Paul,
hope you don't mind me jumping in here; i'm having a very similar issue with some 7T MP2RAGE data (which i denoised first); see attached after an SSwarper run.
did you find a solution to Lysianne's problem? i've run 3 other subjects from this dataset through SSwarper and they finished fine. note that the final anatQQ*.nii image looks okay *at first
by
storrisi
-
AFNI Message Board
hey afni!
where can i find more info about the "FIM" menu in the graphing GUI?
page 25 of afni03_interactive.pdf isn't super helpful
i can probably figure out a lot of its functionality but there's quite a bit there;
any resources that already exist would be greatly appreciated.
thanks!
-sam
by
storrisi
-
AFNI Message Board
hello!
Exciting position available:
Postdoctoral Research Scientist in our lab through Advanced MRI Technologies
and Helen Wills Neuroscience Institute, UC Berkeley.
7T NexGen fMRI and MRI.
-Salvatore (Sam) Torrisi
by
storrisi
-
AFNI Message Board
thanks, Daniel-
yes I'd tried @RetinoProc, but not much and now I'll try again with newfound knowledge. it seems to do a lot, however. my idea was to specify most of the preprocessing with afni_proc and then pick up with the Retino stuff where it leaves off (e.g. I've been inputting pb*.scale* files into 3dRetinoPhase). do you foresee any problems with this approach? i predict t
by
storrisi
-
AFNI Message Board
update again:
3dRetinoPhase -prefix name -spectra -Tstim 20 -phase_estimate FFT -exp pb05.*.scale.niml.dset
seems to work well and replicate what we were getting with mrTools
by
storrisi
-
AFNI Message Board
Hi again gurus
update: so I answered my own final question and yes, 3dNLfim takes *.niml.dset files and I can view results in SUMA. However, I'm not clear how to use the SineWave_AP model properly. I know the freq of the stimuli (10 sec on, 10 sec off) but is there a way to input that so it doesn't need to estimate the frequency parameter (as apparently SineWave_APF would)? The help
by
storrisi
-
AFNI Message Board
Hi there AFNIers-
I'm trying to run a phase (retinotopic) analysis of a simple on-off block design. no expanding rings or rotating wedges; just a simple shape repeatedly seared into early visual cortices. i've run both volumetric and surface analyses of the data with normal GLM block parameters and those worked fine and i can see the shape on the inflated surface. but now i want to d
by
storrisi
-
AFNI Message Board
thanks Justin, that worked! no more Operation not permitted errors on launch.
now what about the system check's evaluation of 3dMVM and R installs.... despite having R installed and a working Rstudio, I'm still getting:
3dMVM : FAILURE
Error in dyn.load(ll) :
unable to load shared object '/Users/torrisi/abin/R_io.so':
dlopen(/Users/torrisi/abin/R_io.so, 6): Library no
by
storrisi
-
AFNI Message Board
Hi RIck
okay i've rebooted and adjusted some .bashrc and .cshrc text and now both afni and suma open. yay. however when i open afni, and as it opens (during splash screens etc), i get this large printout to the terminal:
torrisi% afni
Precompiled binary macos_10.12_local: Jun 30 2020 (Version AFNI_20.1.18 'Otho')
** Version check disabled: AFNI_VERSION_CHECK forbids
Tha
by
storrisi
-
AFNI Message Board
hi again guys
omg i'm an idiot. i hadn't fully installed xquartz, sorry. i may have also messed up some path stuff last night as i tried to troubleshoot, so i'm still getting an error about DYLD_LIBRARY_PATH but overall it's looking better. first i'll paste my current output of afni_system_check, and then at the bottom of this message i'll respond to rick's n
by
storrisi
-
AFNI Message Board
thanks Peter and TIA
well if i re-run "xcode-select --install" i just get:
xcode-select: error: command line tools are already installed, use "Software Update" to install updates
and then if i type
softwareupdate --list
it says "No new software available."
the output of afni_system_check.py is clearly a mess:
torrisi% afni_system_check.py -check_all
by
storrisi
-
AFNI Message Board
Hi guys-
I see some Catalina threads on here but they didn't quite solve my issue.
I have a new macbook running 10.15.5.
I'm installing according to the AFNI instructions and get to this line and see:
torrisi% suma -update_env
dyld: Library not loaded: /opt/X11/lib/libXt.6.dylib
Referenced from: /Users/torrisi/abin/suma
Reason: image not found
Abort
i've changed
by
storrisi
-
AFNI Message Board
ok i just installed the newest AFNI and it works so wonderfully and smoothly. THANKS BOB. i also added:
AFNI_ZOOM_LOCK = YES // NO=don't lock zoomed in panels
to my .afnirc so it's on by default for me now. i so appreciate this!
by
storrisi
-
AFNI Message Board
hey guys-
thanks for the humorous exchange
no need to build new stuff just for me; i realize i'm one of those annoying 'meso-scale' breeds
daniel your suggestion worked and totally satisfies me enough for me now, THANKS!
for anyone listening in:
before you type daniel's command, start afni (i.e. controller A) with
afni -q -yesplugouts
then do the
plugout_drive
by
storrisi
-
AFNI Message Board
hi my beloved AFNI team-
i'm doing lots of zooming-in micro comparisons between analyses and i really gotta get in there to see differences sometimes.
it's obviously great how we can lock 2 controllers 'A' and 'B' in terms of both cross hairs and pval thresholds.
however, is there a way to also lock zoom, pan and especially crop? i seem to be wasting a lot of t
by
storrisi
-
AFNI Message Board
Hi Rick and Priya-
I seem to be experiencing the same thing. I have nothing in my AP script about reml stuff, and even have "-regress_run_clustsim no" added to speed things up. My resulting proc.* script also has nothing in it about REML at all, and yet in the output it looks like 3dREMLfit is being run after 3dD because the "voxel loop" part takes upwards of 10 minutes to
by
storrisi
-
AFNI Message Board
Hi Jun and Daniel-
Just chiming in a little to say that to my own eyes your first set of screenshots looked like the mask was more in the internal globus pallidus and after the shift looks better but still more like the central nucleus of the amygdala... so I'd be careful about the initial input masks. I checked FSLeyes and they don't seem to have the structure, and yes, it's in
by
storrisi
-
AFNI Message Board
ha, amazing! you did that so fast. thanks so much Daniel, it works perfectly.
p.s. unrelated and no biggie but the "-overwrite" option isn't in 3dcalc's help
by
storrisi
-
AFNI Message Board
Hi AFNI team-
how hard would it be to add options to 3dUndump to create a prolate spheroid instead of a regular sphere?
i'd imagine 2 new options would need specification (its semi-axes) as well as the main direction the semi-major axis would 'point'?
just curious and thanks
-Sam
by
storrisi
-
AFNI Message Board
A postdoc position is opening up in the Christian Grillon lab at NIMH:
by
storrisi
-
AFNI Message Board
Page 1 of 2
Pages: 12