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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:
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Sincerely,
AFNI HQ
History of AFNI updates
Page 4 of 4
Pages: 1234
Results 91 - 110 of 110
Hi Gang - Ok, I reduced a subject comparing:
CSPLINzero (0,15,6)
CSPLINzero (0,18,7)
for my 3s TR data. I've attached a screen shot of the results for the first 6 TRs. Red is (0,15,6) and Blue is (0,18,7). I'm not sure I understand why they look so different in the beginning? I thought by including an extra time point, I would retain any differences on the 2nd to last time, but
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mb
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AFNI Message Board
Ok - that is definitely clear then. I did NOT know that stimulus timing would have to be shifted by 1/2 TR if the default option was selected, and of course -- having the stimulus timing right is the most critical issue i can see. thanks again, mb
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mb
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AFNI Message Board
Thanks to you both - Much helpful information. Now I'm wondering which to use? -tzero 0 or the default, which is the mean? In the python script that is suggested for use, it uses -tzero 0. So - then I wonder why the default is different? My design has a 3 s TR, 53 interleaved slices (which I can now confirm, using the -verb) -- any guidance as to which would I want to use, and why? Thanks
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mb
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AFNI Message Board
Hi all,
I'm trying to figure out the -tzero parameter for 3dTshift. In the documentation for this procedure, it says:
-tzero zzz = align each slice to time offset 'zzz';
the value of 'zzz' must be between the
minimum and maximum slice temporal offsets.
N.B.: The default alignment time is the average
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mb
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AFNI Message Board
Thanks for ignoring this, because it turns out I had updated afni since I last used Skullstrip, and I do not have the 64 bit version of fink. So - reading through the threads and realizing I had changed versions etc..... I will install 64 bit version and presumably problem will be solved. In the meantime, if I go back to my earlier afni - Skullstrip works. Sorry to bother,,, thanks, mb
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mb
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AFNI Message Board
Center distance of 35.368508 mm
Padding ...
++ 3dZeropad: AFNI version=AFNI_2011_12_21_1014 (Oct 18 2012) [64-bit]
++ output dataset: ./__ats_tmp__ref_TT_N27_40pad+tlrc.BRIK
Skull Stripping ...
dyld: Library not loaded: /sw/lib/libglib-1.2.0.dylib
Referenced from: /Users/bradley/afni/3dSkullStrip
Reason: image not found
Trace/BPT trap
Error: Failed to create skull stripped brain
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mb
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AFNI Message Board
Also - I was sort of wanting to look more into what actually happens with 3dTshift, in terms of the computations, but I can't see a manual on that -- is it included in some other manual perhaps? thanks, mb
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mb
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AFNI Message Board
I'm puzzled as to why this is listed in the afni.proc.py? It says the default alignment for 3dTshift is the average of the tpattern values, so I'm wondering why the default is changed to -tzero 0 is in this .py shell. Is it the case that we typically don't want to use the default (i.e. mean of tpattern) for 3dTshift? thanks, MB
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mb
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AFNI Message Board
I redid using CSPLINzero and things look good except I was wondering whether there is a way to force zero at the first TR but not the last? That is - conceptually it seems that nothing should be going on during the 1st TR but there could be action at the last -- i.e., if one condition results in longer-lasting changes or something. But - I can't see that that can be done in 3dDeconvolve, rig
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mb
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AFNI Message Board
Hi folks - thanks for your thoughts. It's not a stimulus timing error or anticipation. It doesn't occur in every region where there are significant condition differences, just some -- I guess it could be some motion affecting certain regions? I will try CSPLINzero, though, which sounds like a good option. thanks, MB
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mb
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AFNI Message Board
IRFs - 11 years ago
This question is more of a theoretical question than one of the mechanics of AFNI. When IRFs are computed and plotted, what is one to think of (large) significant differences that occur between conditions on the 1st TR? That is - there is a large difference even before "things can get going". I know the shape of an IRF over TRs is identical to what one would get if you just deviated
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mb
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AFNI Message Board
Hi Daniel - The values for the second sub-brick range from 0 to 350 - I was expecting them to reflect Brodmann areas, which I thought were Areas 1=52. So - I guess I don't understand how the values in the BRIK identify Brodmann areas. I wanted to output the atlas info and then I can compute overlap of significant voxels for all areas at once in other software. thanks, mb
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mb
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AFNI Message Board
Hi Daniel - Hmm. I looked in the first BRIK in the TTatlas file (BRIK=0) and the values are hard to understand, in terms of Brodmann areas? The right half of the brain is labeled from 0 to about 65, and the left half is labeled the same, but preceded by a "2" (i.e. 200-265). Two of the same regions on the right and left would be 40 and 240. But - these numbers don't seem to be rela
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mb
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AFNI Message Board
No - I think hat is my question. But - I dn't have an atlas named TT_Daemon in my afni folder? Is it named something else? When I looked for descriptions of these in the atlas file, I didn't see anything that indicated the Brodmann regions were in a brik. Maybe you are just talking about the generic TT_atlas file???? thanks, MB
TT_N27+tlrc.BRIK.gz
TT_N27_EZ_ML+tlrc.BRIK.gz
TT_N27_E
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mb
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AFNI Message Board
I noticed on FIASCO's website (see below) that it says it distributes a Brodmann atlas in AFNI format (brodmann.tlrc). BUT - when I downloaded Fiasco, there was atlas subdirectory or file included. Does AFNI distirbute its own Brodmann atlas file? I don't think so (from reading the atlas's available in AFNI_atlas_spaces.niml), but I just wondered. Or - are the FIASCO brodmann.tlrc
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mb
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AFNI Message Board
Hey thanks folks - It worked like a charm. Used the TT_caez_ml_18+tlrc (Thanks Isaac) as the -inset in 3dresample (with -rmode NN; Thanks Rick) and one of my BRIKs as -master to create a new file for the atlas with my spatial dimensions. Exported that (3dAFNIto3d) to a .3D file which contained a region number for each voxel in the BRIK -- it did not retain the verbal labels, but it was easy to g
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mb
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AFNI Message Board
Hmm- Yes, I know the atlases are in the afni folder.
But - currently, I get a masked region from an atlas (using whereami -mask_atlas.region), and then use 3dresample to register the atlas region to my data. SO... if I want to output the whole atlas, I have to figure out which file to use with 3dreample (usually, the mask file is used with -inset) so that the atlas regions relate to the spat
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mb
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AFNI Message Board
I often export whole AFNI bricks to other software where I can do other analyses. I was wondering if there is an easy way to output the atlas info for each voxel in a BRIK so that I could do region analyses using that same software. So, I would like the operation to result in something like a 3D file where for each voxel in the BRIK, it would list the region (from one of the atlases) for that vo
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mb
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AFNI Message Board
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