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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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> OK, the error is fixed (I hope) in the latest
> release of AFNI = AFNI_21.2.02 (just released
> now). There was a problem reading files larger
> than 2 GB -- in a different place, this time.
It all works well now - thanks!
by
Damien Mannion
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AFNI Message Board
Hi,
Great, thanks for the update.
I no longer receive the error message in the output of `3dREMLfit`, but the resulting file still does not seem readable:
> 3dinfo err.niml.dset
++ 3dinfo: AFNI version=AFNI_21.1.20 (Jun 28 2021) [64-bit]
** FATAL ERROR: Can't open dataset err.niml.dset
** Program compile date = Jun 28 2021
The file is 2897399991 bytes in size.
If I try
by
Damien Mannion
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AFNI Message Board
Thanks for looking into it!
> So it stops AFTER writing 2.8 GB of the output file?
Yes, that's correct.
> How big is a completed file with 9 input runs?
With 9 runs, it is 899607339 bytes.
> Then multiply by 29/9 to estimate the size of the desired file?
That gives 2898734759 bytes.
> The result has been computed in memory, and the problem is converting it to
by
Damien Mannion
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AFNI Message Board
Hi,
I'm receiving an error with the `-Rwherr` option to `3dREMLfit`.
The program seems to run OK, but the residual dataset is not readable and there are the following messages in the program output:
NIML: write abort P
NIML: write abort s
** failed to write NIML output file './err.niml.dset'
** write_niml_file failed for './err.niml.dset'
++ Output dataset ./
by
Damien Mannion
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AFNI Message Board
Hi,
> It sounds like when using it, which should be
> done, there is no problem---is that correct?
Yes, that's right - it works when using the "-NIFTI" option. I haven't been using the "-NIFTI" option in the past (which used to work fine), so I have a set of participants with SUMA directories that don't contain that form of output (and code that use
by
Damien Mannion
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AFNI Message Board
Hi,
I am having a problem with @SUMA_Make_Spec_FS that I hope you can help me with.
I have noticed that after running the command (from the base of the relevant FreeSurfer output directory):
@SUMA_Make_Spec_FS -sid p1032
that some of the files in the SUMA directory that is created (e.g., "T1.nii") are out of alignment with the "p1032_SurfVol+orig" file in that directo
by
Damien Mannion
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AFNI Message Board
A position is now available for a full-time Postdoctoral Research Associate to work on research being conducted on human visual perception in the School of Psychology at UNSW Sydney, Australia. The project position is fixed-term for 18 months.
The role will involve conducting research related to the project "Foundations of the tolerance to illumination variation in human visual cortex&quo
by
Damien Mannion
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AFNI Message Board
Hi,
I am using SurfDist to calculate the shortest distance between nodes on a pial surface, with the "-Graph" option. In terms of the underlying computation, would it be correct to say that SurfDist (using "-graph") determines the shortest distance between nodes using a typical implementation of Dijkstra's algorithm?
Thanks,
Damien.
by
Damien Mannion
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AFNI Message Board
Hi,
I am having the same problem as is described here - moving the threshold slider causes suma to crash. Was a solution found?
Below is the crash log I get after running 'suma', View -> Object controller, then move the threshold slider.
Thanks,
-damien
*********------ CRASH LOG ------------------------------***********
Fatal Signal 11 (SIGSEGV) received
..........
by
Damien Mannion
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AFNI Message Board
Ziad,
Using x2go on a local network with a SUMA window size of 750x790 (on 'suma -i ld120') gives:
++ Notice SUMA_input (SUMA_input.c:4171 @14:52:43):
Timing Display speed
(20 displays):
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
++ Notice SUMA_input (SUMA_input.c:4211 @14:52:46):
Elapsed time: 2.653892 seconds.
7.54 displays/second.
In Polymode 1, rendere
by
Damien Mannion
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AFNI Message Board
The RSS feed seems to be still down (the link returns a 404 not found) - could it please be restored, if possible? Thanks.
by
Damien Mannion
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AFNI Message Board
Great, thanks Ziad! No, I don't need anything other than ABS display of complex data.
by
Damien Mannion
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AFNI Message Board
Hi,
I'm trying to run 3dDFT on a surface file but I'm running into some problems. Running 3dDFT prints a lot of '** GBMMP, bad dtype' errors to the screen, but outputs a file OK. If I load the file into SUMA, it looks like the ABS frequency spectrum I would expect. If I try and extract the phase using 3dcalc, though, the resulting file looks identical to the ABS. I'm w
by
Damien Mannion
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AFNI Message Board
Oh, sorry. The censoring is certainly simpler. Would you recommend I still do it in two steps, a 'nodata' step with censoring to get the stimulus design matrix and then a processing step where I include baseline polynomial regressors and the output of the first step? Otherwise, including the polynomials when censoring removes the start of their timecourse and they are no longer mean-zer
by
Damien Mannion
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AFNI Message Board
Ok, I'll continue with the '-stim_file' approach - thanks
by
Damien Mannion
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AFNI Message Board
Hi,
I have a query about the recommended approach for handling events with onsets that are prior to the data but close enough that their response has an influence.
For example, I have an ABAB..AB block design where I want to discard the first and last blocks - so that data at t=0 is the start of the second block. But the first few timepoints in the resulting data include the influence of th
by
Damien Mannion
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AFNI Message Board