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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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Hello AFNI team,
Is there any way we can save a layout of windows such that we can relauch it easily. For example, I have some complex set of afni windows layed out as in the attached screenshot. I'd like to be able to launch it from command line without having to rebuild it from scratch--especially the graph "double plot" with many "Dataset #N". The dream would be to
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Sébastien Proulx
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AFNI Message Board
Makes a lot of sense. I'll keep that in mind. Thanks again for the help Daniel!
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Sébastien Proulx
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AFNI Message Board
Thanks a lot Daniel, that worked!
Also, just as a note for anybody trying to do similar stuff, I ended up doing a dummy pass of 3dNwarpApply (3dNwarpApply -prefix $out -nwarp 'IDENT(session1+orig)' -master session1+orig -source session1+orig -interp NN) on everything before doing anything else. I started doing that sometime ago after encountering problems using 3dNwarpApply to apply
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Sébastien Proulx
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AFNI Message Board
Dear Afni experts,
I am trying to align EPIs of a brain that was scanned in 2 different session. The EPIs of the two sessions have the exact same acquisition grid dimensions, and the same position relative to the brain, since they were prescribed with autoalign on a Siemens scanner. So the brain position is well matched in the two image grids, and this is all I want because one of the things
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Sébastien Proulx
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AFNI Message Board
Thanks a lot for the debugging me!!
Just a note: I found out that 3drefit worked fine directly on my mydset.nii.
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Sébastien Proulx
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AFNI Message Board
Dear Afni developers,
Previously, I was using 3dQwarp on oblique PLUS-MINUS phase-encode direction data for distortion correction within a custom semi automatic pipeline, and it worked fine.
I recently updated my afni from the 32-bit version to the 64-bit version (see: ) to fix some other problem with warp inversion in 3dQwarp.
Now, 3dQwarp produces warped images on grids with the same d
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Sébastien Proulx
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AFNI Message Board
To summarize the side issue:
-@update.afni.binaries -package linux_xorg7 killed my afni because I have a 64-bit system, and I understand this installed the version for 32-bit
-@update.afni.binaries -package linux_xorg7_64 resurected my afni.
-See Rick's last post on this thread
On the main issue:
-Updating my afni with the proper package fixed the problem 3dNwarpApply not properly inv
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Sébastien Proulx
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AFNI Message Board
Mmm, the update went through without error, but for some reason I cannot launch afni anymore.
The new binaries were installed in ~/abin, which is still in my PATH, but for the command I tried (e.g. afni or 3dcalc), I get
bash: /home/bass/abin/afni: No such file or directory
Similar thing in tcsh.
The @* commands seem to work fine though.
Tried rebooting, no luck.
Tried rerunning
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Sébastien Proulx
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AFNI Message Board
afni -ver
Version AFNI_2011_12_21_1014
[]
I'll try
@update.afni.binaries -package linux_xorg7
and let you know
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Sébastien Proulx
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AFNI Message Board
I just stumbled on something weird that may be worth to report.
With 3dQwarp, I non-linearly register two EPI images that were acquired with the same parameters except for the direction of phase encoding (for EPI distortion correction), and the output images are as expected half-way between the input images:
3dQwarp -overwrite -prefix funMean.nii.gz -base distRef.nii.gz -weight distRef-mask
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Sébastien Proulx
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AFNI Message Board
Ok. After fooling around a little, I think I could implement your suggestion in 3dttest++ by putting the regression matrix into a file I feed to 3dttest++ through -covariates. Details are explained below, but before that, I have a burning question. Is the limit of 31 covariates an absolute one? I am afraid that for my purpose here, I am "completely deranged". Since I am specifically int
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Sébastien Proulx
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AFNI Message Board
Thanks for the quick reply Gang!
I should have specified that it is the shape of the hemodynamic response I'm trying to get, so 3dttest++ doesn't seem appropriate.
I don't mind phase being correlated with my regressors. The idea is to implement Menon's phase regression method (Ravi Menon, Mag Res Med 2002) in a slightly different way. Since phase correlates with magnitud
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Sébastien Proulx
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AFNI Message Board
Dear Afni gurus,
I have BOLD signal time series of both magnitude and phase, acquired during a visual task. I'd like to analyse task-related magnitude response while regressing out the phase signal just as we can do for movement parameters with -stim_base in 3dDeconvolve. The thing is that contrary to movement parameters, which are the same for every voxels, the phase time series to regre
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Sébastien Proulx
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AFNI Message Board
Dear Afni Gurus
My compulsive nature had me push a little more on this today.
First, I simplified the problem by comparing the outputs of 3dQwarp and 3dNwarpApply without any motion correction (or more precisely by doing motion correction independantly in a first step and not using -affter in 3dNwarpApply). That made me realize that I should not use the 'IS:' operator in -nwarp, a
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Sébastien Proulx
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AFNI Message Board
Dear Afni experts,
I'm trying to combine motion correction from 3dvolreg and deformation correction from 3dQwarp (with the -plusminus option for the use of a reference with a reversed phase encoding direction (blip up and blip down)) in one interpolation step with 3dNwarpApply.
I would have expect that applying the correction sequentialy of simultaneously would yield very similar images,
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Sébastien Proulx
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AFNI Message Board
Thanks for the indications!
I had a look at the model_*.c file, and even if I've never worked with C before, I think I understood a bit how this works, especially when looking at the simpler model_sinewave_ap.c. But I got totally stuck at understanding how time and event times are defined and convolved in model_conv_diffgamma.c, which is the model I need.
I should also mention that I a
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Sébastien Proulx
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AFNI Message Board
Dear Afni gurus,
I tried to use 3dNLfim with sub-TR event timing, and failed. It seems from this post (http://afni.nimh.nih.gov/afni/community/board/read.php?1,142226,142363#msg-142363) that, at least at the time of the post, TR-locked events are required. Is handling of non-TR locked events implemented now? I suspected it might be through the -time argument, but I couldn't make it work.
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Sébastien Proulx
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AFNI Message Board