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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 yes. I see. Total volume for stat1. Then total volume for stat2 etc. thanks. mb
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I am reading a binary BRIK into a program. I know that for a xyz volume, x moves fastest, then y, then z. But - I'm wondering about the stats (e.g. dimension #4) - are those moving the fastest? If I have 4 stats in a BRIK file - how would I access each of them correctly for each voxel, in terms of the computation? thanks, mb
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Thanks Rick & ptaylor - The drive plugin worked well and we were able to what we wanted. thanks again, mb
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thanks Rick & ptaylor - I'm going to check it out. Can't say I've "driven" AFNI, before,so I'll take her for a ride....
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Hi folks - I would like to take overlay stats form a functional analysis on anatomical data for each of hundreds of participants, and then select 1 2d image from the anat brik to save and print as .jpg. So - I will obviously use a shell, rather than the AFNI viewer to do this.
I have looked into a number of different 3d programs that will let me select one 2D image from a 3D anatomy BRIK, but
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Hmmm. I had asked this question awhile ago but just got around to checking today. I am doing the timeshifting and volume registration using the following the align_epI_anat.py. As I understand it, the default is to DO timeshifting (i.e. -tshift on -volreg on). So - I just give it the options for each routine.
#align_epi_anat.py -anat "$sub".struc+orig -epi "$sub".image+ori
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OK - Reading the Cox, Reynolds, & Taylor draft - in Figure 1, it seems to say the MEDIAN a,b,c values across subjects was used??
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I was looking at the suggested processing stream for using 3dFWHMx and 3dClustSim and just wanted to check and see if I've got it straight.
1. Using -errts in 3dDeconvolve (for instance) get residuals for each subject.
2. Run 3dFWHMx on EACH TR in the errts file for each subject, excluding trails that are censored.
3. Append the 3 output parameters (a,b,c) to a .1D file for each subject
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Just wondering if there is an AFNI bootcamp scheduled for fall 2016 or in 2017 sometime?
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I guess I could look through the python script and get this answer but just wondering if, when you specify tshift and vr whether the output files labeled .tshift and .vr have the other operation -- that is, is the .tshift BRIK also volume registered? is the .vr BRIK also timeshifted? Or, does it depend on order -- ie. if you volreg first does the tshift operation use that volume? thanks, mb
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Thanks Rick - Nice. Yes, I see the difference in the parameters - it was the stats that were the same (at least for 1 sub) - but I can imagine why that would occur given those parameters and the data. thanks again, mb
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Hmmmm... So this thread made me a little puzzled. the "duration" parameter in Block is supposed to be stimulus duration, right? So if one had a 3s TR and a 6s stimulus presentation (e.g. 2 TRs) - one would use Block(6,1) right? I just ran Block(6,1) and Block(3,1) on data like this (single subject) and the results are identical. I'm not sure I understand why but is that what one
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Thanks for the info. And yes - I meant that AFNI does per-voxel time series normalization, not normalizing all voxels. Most psychophysiological measures (e.g. ERPs, electrodermal, cardiac, etc.) use a baseline immediately preceding stimulus onset to control for things like local drift, habituation, etc even if changes are not huge. Even with what you have said here, it makes sense to me to use
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When discussing PLS methods of analyzing fMRI data, McIntosh et al. (2004) normalize the data for each trial with respect to the signal at the onset of a trial, rather than using the mean signal in a voxel across the time series (which is often included in AFNI examples) to make it more comparable to an ERP measure (which is always deviated from a local pre-trial baseline). Just wondering if this
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Yes - that was the issue. Needed to make a copy; Now middle button works which is fine.. thanks alot, mb
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Ok - thanks now I see it. But it currently says "pan" and it is greyed out. When I select "zoom", it zooms in, and then pan is not greyed out but when I click it, it never changes to pen - is it supposed to? thanks, mb
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Thanks - I'll try that. But when I look for "pen" in the "drawing window" - I don't see it? By drawing window do you mean the draw Dataset window? Or the image window that I want to draw in?? thanks much, mb
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In the Plugins, it says that a region should be drawn by using the middle button of the mouse. But - my middle button doesn't do anything. I'm running on a Mac. Just wondering if any one has any ideas. thanks, mb
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Oh yes - right. I forgot about the glt commands....i *thought* i had done this before,,,, thanks a lot, mb
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If I use 3dDeconvolve (CSPLINzero), I can get the Ftests for whether each coefficient is different from zero. Is there a way to test, for each subject, whether 2 of the coefficients are statistically different? thanks, mb
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fim - 9 years ago
Early on in AFNI development, I believe I had a program called fim which would open a 3d+time file and interactively you would select an ideal waveform and it would then show you all the voxels that matched that waveform. Is it still available in AFNI? 3dfim seems to do this, but without displaying the image in real-time, which is what I was looking for. thanks, mb
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Please disregard - I temporarily lost my mind. The anatomy is already aligned.... thanks, mb
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I have run the py program algn_epi_anat.py for one data run. Now - I'd like to align the epi from a second run. But - I don't think I have to redo all the stuff with the structural image. Looking at the .py script, though, it's not easy for me to see which parts I need to keep to align this new epi data to the same anat file? Is there a .py script for this, or is there is an easy
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I was wondering if the original fim program is still part of afni -- you would just give it a file to read and it would open the file in 3D (I think it was 3D) and you could click on a voxel as a reference function and it would show all the voxels in volume that correlated with that voxel. It was interactive -- I know 3dfim, for instance, would do the same thing, but create files instead of inter
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Wow - that's very thorough Rick - appreciate it. And sorry about using the wrong spec for auto_tlrc - in fact, I used TT_N27.
I will digest the rest of what you said, but I *think* I understand the ins and outs. Yes, I think I am in TLRC space......Thanks much, mb
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Thanks for the joke. Now - just a couple more questions about coordinates, sorry.
1. I have transformed my data using @auto_tlrc CA_N27_ML -- so this data would be in MNI space, right? or wrong?
2. When I look at these .tlrc images in afni, I get, let's say RAI of 13 64 -4 -- this is ... in Talairach space, right?
3. When I get the CM of each cluster using 3dCM - it gives me RAI i
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Thanks -- but wouldn't RAI be LPS in packages that determine order by the most positive dimension?? Just wanted to make sure I'm understanding what you're saying -- increasing from inferior to superior in both??
Also - I said MNI coordinates instead of spaces because several papers I have report "MNI coordinates". When this is reported, does this mean we don't
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Looking around the internet and afni for info on the different coordinate systems, so far this is what I have found -- is it correct?
1. RAI is DICOM format and default for afni.
2. LPI is SPM orientation.
3. LAS is the radiological convention and used in ANALYZE.
4. RAS is the neurological convention and used in Talairach, MNI.
Then - is there some standard or preference for use in fMRI
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OK Thanks Gang - That makes sense. I do have baseline (fixation) throughout... best, mb
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