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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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Two questions about to3d:
1) Is there a way to force the interactive GUI to launch from the command-line? I can't seem to figure out how to get it to launch and I'd like to play with some of the values during reconstruction.
2) I'd also like to know if it's possible to force a slice thickness during reconstruction. I thought it was a to3d or a dimon option, but I don
by
Adam Greenberg
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AFNI Message Board
Hi Rick,
Thanks so much for your response.
This all seems reasonable. I'm going to give it a shot without using afni_proc.py. I've got scripts I use that essentially replicate that script, anyway. And, this will allow me to make important changes where needed.
One quick follow-up I have off the top of my head
What changes would you expect me to have to make to the motion param
by
Adam Greenberg
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AFNI Message Board
Just thought I'd bump this up in case anyone has some thoughts they can share on this.
Thanks a lot,
Adam
by
Adam Greenberg
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AFNI Message Board
Hi Rick,
I'm just restarting this thread because I'm dealing with some new sparse sampling design data and would like some help. First, is there a "standard" way that you've developed to deal with these gaps in the acquisition? If not, can you please outline (or send me a link to documentation) your current feelings on the best way to analyze these data?
Here are so
by
Adam Greenberg
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AFNI Message Board
Hi guys,
I ran the following command:
SurfSmooth \
-met HEAT_07 \
-spec std.141.MusicCog_DDA_lh.spec \
-surf_A std.141.lh.smoothwm.asc \
-surf_B std.141.lh.pial.asc \
-input MusicMain1_RASuN_lh.niml.dset \
-blurmaster MusicMain1_RASuN_lh.niml.dset \
-detpoly_master 4 \
-output MusicMain1_RASuNS_lh.niml.dset \
-target_fwhm 3 \
-bmall \
-cmask "-a MusicMain1_RASuN_lh.niml.dset -
by
Adam Greenberg
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AFNI Message Board
Hi Ziad,
Ok, the system admin upgraded to the latest version of AFNI. When I run the following:
@SUMA_Make_Spec_FS -sid MusicCog_AER -debug 2 -GIFTI
the script now hangs on a 3dmerge command. Specifically, at this point:
3dmerge -1rank -prefix aparc+aseg_rank.nii aparc+aseg.nii
Program 3dmerge
++ 3dmerge: AFNI version=AFNI_2011_12_21_1014 (Jun 17 2014) [64-bit]
Any thoughts?
T
by
Adam Greenberg
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AFNI Message Board
Hi Ziad & Rick,
Thanks for your responses.
Ziad: when I run with the -GIFTI switch I get an "invalid option" error; they must have an old version of
AFNI running; I'll have to get the server admin to update to newer binaries
Rick: I don't see a copy of MusicCog_AER_SurfVol+orig located anywhere. I don't think the script got that
far. I was just running thes
by
Adam Greenberg
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AFNI Message Board
Hi AFNI folks,
I'm running @SUMA_Make_Spec_FS for the first time in a while. Here's the command I'm using:
@SUMA_Make_Spec_FS -sid MusicCog_AER -debug 2 -neuro -use_mgz
After a minute or so, it looks like a to3d command is executed, at which time to3d is launched and then
the script just hangs. Doesn't seem to have crashed, but it looks like to3d is still working. He
by
Adam Greenberg
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AFNI Message Board
Hi Bob,
I'm wondering the extent to which this boot amp will cover some of the newer
(more advanced) AFNI features added over the past few years such as 3dLME,
3dREMLfit, granger causality, DTI, 3dMVM, 3dMEMA, ETC.
Or, should we expect that this course will start at first principles of AFNI, and
not quite get to these more advanced issues?
Thanks, Adam
by
Adam Greenberg
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AFNI Message Board
One more quick update. If I change the pial surfaces LDP to SAME,
issue number (1) in my original post is resolved (though I don't think
the nodes correspond across surfaces anymore). But, issue (2) above
is unchanged.
Thanks,
Adam
by
Adam Greenberg
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AFNI Message Board
Hi Rick,
Yeah, I had switched those thinking that there was maybe a naming issue
with those surfaces. But, that didn't solve the problem, unfortunately. I get
the same issue when they're correct (SurfaceName & LDP are both the same
hemisphere).
I've found another possible cause of this, though. For some reason, when I
use the -niml switches on the suma and afni comman
by
Adam Greenberg
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AFNI Message Board
Hi AFNI gurus,
I've got a set of surfaces that were generated in BrainVoyager and exported to
GifTi format. I have LH & RH pial, smoothwm, and inflations. I have used quickspec
to create a spec file so they can all be read in and associated with one another.
But, I'm getting some strange behavior:
1) When I read in the pial surfaces only, using the -i_gii switch, they loo
by
Adam Greenberg
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AFNI Message Board
Hi AFNI folks,
I've got two anatomical datasets I'm aligning using the align_epi_anat python script. All is
fine with the alignment. However, I've also got a set of ROIs that need to be aligned to the
same target anatomical. This ROI dataset is an anatomical mask with integer values shoved
into each voxel that's part of an ROI (5 for V1, 10 for V2, for example). So, I th
by
Adam Greenberg
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AFNI Message Board