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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
I'm actually not sure I've seen anyone successfully attach an image to this message board in the last two years, though not for lack of trying. Are there permission requirements? Maybe that control should just go away.
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Isaac Schwabacher
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AFNI Message Board
Looking at it again, I suspect that your script is either not succeeding in ordering the inputs, or to3d is ignoring the order and sorting the inputs back to the wrong order. Try renaming the images or using Dimon with -dicom_org.
Isaac
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Isaac Schwabacher
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AFNI Message Board
Are your images by any chance numbered like this? image_1
image_10
image_100
image_101
image_102
...
image_109
image_11
image_110
image_111
...
image_119
image_12
image_120
...
image_19
image_2
image_21
imagw_22
...
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Isaac Schwabacher
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AFNI Message Board
Speaking of version control, having a GitHub page for AFNI would be amazing.
Isaac
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Isaac Schwabacher
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AFNI Message Board
By the way, my use case was aligning a field map image to a DWI image; the B0 images are pretty T2-like and the field map magnitude image is somewhat T1-like, so I just let it run with the anat->epi defaults and the results are looking pretty good. Thanks!
Isaac
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Isaac Schwabacher
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AFNI Message Board
Hi folks,
I needed align_epi_anat.py to handle NIfTI -child_anat datasets, so I patched it. Here's the patch for upstream:$ align_epi_anat.py -version
#++ align_epi_anat version: 1.47
$ diff --context ~/abin/{auto_backup.linux_xorg7_64/,}align_epi_anat.py
*** /home/schwabacher/abin/auto_backup.linux_xorg7_64/align_epi_anat.py 2014-08-23 20:22:16.000000000 -0500
--- /home/schwabache
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Isaac Schwabacher
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AFNI Message Board
Why not terminate the process without a traceback?
EDIT: We can avoid the traceback by exiting success, as `cat` does here: $ (cat <<EOF
> hello
> world
> EOF
> echo 1>&2 $?) | head -n1
0
hello
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Isaac Schwabacher
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AFNI Message Board
Maybe AFNI should just drop SIGPIPE from the list of signals that trigger a traceback, since it doesn't usually indicate that something went wrong.
by
Isaac Schwabacher
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AFNI Message Board
Maybe to3d will stop segfaulting now at the end of every execution, after writing the output. :)
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Isaac Schwabacher
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AFNI Message Board
NEVER log into your computer as root!
In general, you don't want to give programs permission to do more than they need to do, because there are a lot of things you don't want to do, whether it's by mistake or because an attacker is trying to take over your system. Other accounts on your computer (even administrator accounts) have limits on what they can do, but root can do anyt
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Isaac Schwabacher
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AFNI Message Board
It's fixed. That'll teach me to update before I report a bug. :/
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Isaac Schwabacher
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AFNI Message Board
I'm using linux_xorg7_64 and updating to latest right now. If you build that one and this doesn't work, I'll update again and we'll see how that goes. I should probably just maintain an install from source, but that's been a tremendous pain in the butt in the past.
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Isaac Schwabacher
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AFNI Message Board
Hi Gurus,
I discovered while trying to visualize the phase of the FFT of our EPI data that setting a 3D+time RGB dataset as an overlay in the AFNI viewer causes memory corruption. The number of errors reported (which may or may not correlate with the actual amount of memory affected) each time the graph window is opened or closed seems to increase linearly with the total number of RGB subbric
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Isaac Schwabacher
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AFNI Message Board
Hi again,
I'm still getting a similar error, this time without the `;Secure` part:
$ \@update.afni.binaries -d
-- have AFNI binaries under /home/schwabacher/abin
-- install dir: using existing /home/schwabacher/abin
-- attempting to install package linux_xorg7_64 under
install dir: /home/schwabacher/abin...
-- have install dir
++ working in new temp dir, .tmp.install
++ getti
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Isaac Schwabacher
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AFNI Message Board
Hi Gang,
I'm having trouble getting 3dLME to run with a GLT involving a quantitative variable. The problem seems to be that `3dLME -help` instructs me to code a GLT testing the effect of a covariate `runidx` by coding `-gltCode 'runidx :'`, but this means that lop$gltCode[] is `[1] "runidx" ":"` at 3dLME.R:568, so that the first argument to `gltConstr` in gl
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Isaac Schwabacher
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AFNI Message Board
There are a bunch of AFNI programs written in R (3dMVM, 3dLME, 3dMEMA) and they have to read and write datasets somehow. If you go poking around in their code I bet you can figure something out.
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Isaac Schwabacher
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AFNI Message Board
I had thought that Dimon had this behavior because there was no DICOM field containing the slice timing information, but I recently discovered in the nibabel documentation that there's a tag Temporal Position Identifier (0020,0100) that seems to contain the slice timing. Oddly enough, however, our GE scanner fails to populate this field. Is there a history behind this?
Isaac
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Isaac Schwabacher
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AFNI Message Board
Hi gurus,
I don't know enough to be able to tell whether this is actually a security issue, but if it is I imagine you want to know about it.
$ \@update.afni.binaries -d
-- have AFNI binaries under /home/schwabacher/abin
-- install dir: using existing /home/schwabacher/abin
-- attempting to install package linux_xorg7_64 under
install dir: /home/schwabacher/abin...
-- have inst
by
Isaac Schwabacher
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AFNI Message Board
Dimon seems to think that file 1.2.840.113619.2.244.3596.11020768.13034.1318008598.975 is broken in some way. Is that file supposed to be there? Is it the same size as the other files?
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Isaac Schwabacher
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AFNI Message Board
If you just want to change the display, you can left click on the color bar in the overlay panel to invert it.
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Isaac Schwabacher
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AFNI Message Board
Hi gurus,
I am not going to get sucked down the rabbit hole again going after a segfault that doesn't appear to affect the actual output of the program, but before I noticed that to3d had written its output properly, I dug into the code enough to notice that the stack trace given in the error message is impossible:
% to3d -quit_on_err -prefix fingertap \
-time:zt 40 135 2.0sec a
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Isaac Schwabacher
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AFNI Message Board
Glad to help. My text editor also displays line-continuation backslashes in a different color from other backslashes, and it helps a lot. Maybe you just need to mess with the color settings a little-- white versus hot pink is a lot easier to distinguish than black versus dark blue! :)
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Isaac Schwabacher
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AFNI Message Board
This sounds like the line might not be continuing properly from here:
3dMEMA -prefix SubjectiveFamiliarityHit6vs5 \
-jobs 16 \
-max_zeros 0.25 \
-missing_data 0 \
-set 6vs5 \
SS01 SS01/'decon_SubjectiveFamiliarityHit456_twottests_smartblur4_masked_ANTS+tlrc[3]' \
SS01/'decon_SubjectiveFamiliarityHit456_twottests_smartblur4_masked_ANTS+tlrc[4]' \
SS02 SS02/'decon_S
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Isaac Schwabacher
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AFNI Message Board
I'm not an expert, but it sounds like your errts dataset is corrupted, which you could probably check by trying to open it in the viewer normally.
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Isaac Schwabacher
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AFNI Message Board
One thing that can go wrong if you're using TextEdit is that as of OSX 10.9, it inexplicably converts quote characters into non-ASCII "smart quote" characters even when editing plain text. It will also convert multiple consecutive dashes into non-ASCII em- and en-dash characters, but it looks like it doesn't convert the minus in a negative number, so purely numeric text is pr
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Isaac Schwabacher
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AFNI Message Board
3dTstat has a (new?) -argmax1 option precisely for this case; otherwise your first ROI will be assigned the value 0 and disappear. Also note that unless AFNI_PATH_SPACES_OK is YES, you can concatenate the ROIs on the command line like so:
$ 3dTstat -argmax1 -prefix ROI_SET.nii.gz "ROI_FILE_01 ROI_FILE_02 ROI_FILE_03 ..."
If AFNI_PATH_SPACES_OK is YES, you can still concatenate a
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Isaac Schwabacher
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AFNI Message Board
The infant-2yr-withCerebellum.nii.gz dataset is pitched forward a little bit relative to the other infant-2yr-* datasets. It's easy to see just switching between the datasets as underlays; compare to infant-2yr-withSkull.nii.gz and infant-2yr.nii.gz, which are in perfect alignment with each other. If it turns out that it's right in the source tarball and wrong in my local copy, I'
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Isaac Schwabacher
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AFNI Message Board
Hi Gurus,
I was poking around in the atlases and noticed that one of the images associated with the infant-2yr atlas appears to be misaligned.
Version AFNI_2011_12_21_1014
[]
HTH,
Isaac
by
Isaac Schwabacher
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AFNI Message Board