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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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Hi Daniel,
I WANT to flip L to R in some of my sessions (because inactivation hemispheres were randomized).
How can I easily mirror flip a stats BRIK around the L|R plane?
Thanks,
Peter
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PeterK
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AFNI Message Board
Sorry, let me be more specific:
I take the inverse (zeros become 1s; 1s become 0) of M v. baseline thresholded at p = 0.01, (or p = 0.005), and exclude those voxels in 3dLME or 3dANOVA by specifying this inverse mask with the line "-mask inverseM+orig."
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PeterK
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AFNI Message Board
Thanks Bob,
I have modeled each regressor (M, 1, 2, and 3), and created mask (M vs. baseline). Remember, in a given trial M occurs, with variable delay, before 1, 2, or 3.
Yes: compute the amplitude of M, and 1, 2, and 3 separately.
What do you think?
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PeterK
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AFNI Message Board
Hi AFNI friends,
What is conventional wisdom regarding masking (or not)?
I have 4 modeled regressors. In a single trial, M occurs before 1, 2, or 3.
M is the result of a generic somatosensory/motor process. Responses to 1, 2, or 3 include the aforementioned generic somatosensory/motor process, but also include additional, distinct, sensory responses.
Think of reaching (M), versus re
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PeterK
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AFNI Message Board
Thanks Gang,
I've run a couple models and they "work" but that doesn't mean they are correct, or correctly implemented. We can discuss why or why not Monkey must be included as a fixed effect, but this is the standard in the field (of monkey work, with limited numbers of monkeys).
What is the correct syntax for Session nested in Monkey? I've run it both ways, one wa
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PeterK
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AFNI Message Board
Thanks Gang, this is coming together...
We model monkey to account for differences (and to see if there is an outlier); but the flip-side if this is that this factor hopefully "soaks up" variance attributable to monkey.
I still want to confirm my nesting argument is correct.
I want Session nested in Monkey (but note session must be called 'Subj'):
I think this is h
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PeterK
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AFNI Message Board
Thanks Gang,
This is going to get confusing in terms of what you and I are really talking about. We only have 3 subjects (monkeys), that's why we need to run multiple sessions / subject. I think I have to turn the scripting upside down a little to get it to work for this scenario, follow me through...
My columns are really:
Session Monkey Taste Hydration InputFile
Session is the
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PeterK
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AFNI Message Board
Hi AFNI crew,
I am trying to implement an analysis in 3dLME and I would like some guidance setting up the model and random effects, and nesting.
With limited numbers of subjects, we run multiple sessions / subject. I want to nest session within subject.
I want to assess the interaction between Taste and Hydration.
I have:
5 sessions (the random effect)
3 subjects
taste: 3 levels
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PeterK
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AFNI Message Board
alright, great! I am running the code now...
PS You may have compromised your identity just now, as your original message was from one "Bob Cox". Now we know!
by
PeterK
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AFNI Message Board
Thanks Bob,
I think this is the information you were pointing out:
Stim[2..7] = means put +1 in the matrix for lags 2..7 of Stim
Therefore, given:
Stim_a[0] = is the main beta from the output of AM2 for Stim_a
Stim_a[1] = is the secondary beta from the output of AM2 for Stim_a
Stim_b[0] = is the main beta from the output of AM2 for Stim_b
Stim_b[1] = is t
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PeterK
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AFNI Message Board
Hi AFNI gurus,
I am doing some analysis with AM2. I've been using afni.proc.py to do it.
When I write the gltsym lines, what contrasts am I looking at?
Is it the primary regressor or the accessory regressor?
I want to create a contrast between the accessory regressors. How can I do that? Is there a way to index with the gly_sym line?
Thanks, Peter
by
PeterK
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AFNI Message Board
Hi Rick, I am getting more or less the same error (below). I am trying to:
-regress_stim_times Times_Values_v4/ChoiceTime_ValEst_v2.1D \
Times_Values_v4/ViewTime_ValEst_v2.1D \
Times_Values_v4/Fluid_Delivery_alltypes.1D \
-regress_stim_types AM2 AM2 times \
-regress_stim_labels Ch_Val Vw_Val REW \
-regress_basis 'BLOCK(1,1)' \
It creates
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PeterK
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AFNI Message Board
Hi All,
Anyone using SUMA on a linux machine? I suspect I may have some issues with my linux machine, since I can view the same files from a mac (where I had to create them).
If I give SUMA the spec and subject volume files, I get a black SUMA screen with 3D crosshairs, though I can see the surface in the AFNI window mapped onto the volume. It toggles through the surfaces with "."
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PeterK
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AFNI Message Board
Hi Rick,
> Censoring outliers is done in afni_proc.py using the -censor_outliers option.
I have done this. I used the output of 3dvolreg to make a censor file.
> But if it is just one part of the brain that shows the outliers,
My question is: Is volreg able determine misalignments in part of the brain? That's what my "diff map" is showing.
> what would you want
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PeterK
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AFNI Message Board
I have found some motion anomalies by subtracting a time-shifted EPI from itself; TR5-TR4, TR6-TR5, TR7-TR6 etc...
If there is no motion between TRs, the difference images should be near zero values. Some parts of my difference images show movement in one part of the brain, while the remainder of the image values are near zero.
Is volreg picking up on this? Perhaps not; in plane motion?
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PeterK
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AFNI Message Board
Great - That is it!
Where do I change the type of orientation AFNI starts with? I would like to see only a coronal image on open. Is that in the AFNI_STARTUP_SCRIPT... where is that, am I supposed to write my own?
Thanks, Peter
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PeterK
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AFNI Message Board
Hi Rick,
file_tool -test -infiles ~/.afnirc
** failed to check size for file '/home/lab/.afnirc'
Hmmm... why is it looking in lab?
which afni
/home/peterk/abin/afni
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PeterK
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AFNI Message Board
Thanks Peter,
I have such a file, but AFNI does not make use of it. Maybe it's not in the right place?
My .afnirc file is in /home/peterk
My copy of AFNI is installed in /home/peterk/abin
I run AFNI here: /data/fMRI
Any thoughts? It's set up as a server so perhaps there is a file structure AFNI is not expecting.
Peter
by
PeterK
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AFNI Message Board
I am running AFNI on a linux system (Ubuntu).
How do I get the environment variables to "stick" - nothing I change is maintained.
I remember hearing there was something specific I needed to do - perhaps edit a startup file?
Thanks, Peter
by
PeterK
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AFNI Message Board
Hi Rick, I ran the following command:
align_epi_anat -cost lpa -dset1 HIRESANAT -dset2 SESSIONANAT -partial_coronal -dset2to1 -volreg_method 3dvolreg -dset1_strip None -dset2_strip None -suffix NEW -child_dset2 SESSIONEPI
It spit out an aff12.1D file. Does this file have the motion parameters in it? It didn't spit out any other files that might have the volreg info in it, just the ali
by
PeterK
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AFNI Message Board
Thanks Rick,
> Applying separate anat/EPI alignment per run is on my todo list, at least. Dealing with multiple anatomies is not.
I have 1 high resolution scan, and a lower-res anatomy taken with each session - is this what you mean by multiple anatomies?
>...stick with your working pipeline, using align_epi_anat.py for alignment through volreg
Currently, I use align_epi_anat to al
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PeterK
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AFNI Message Board
Has anyone had sucess implementing complex align_epi_anat commands within afni.prof.py?
Does afni.proc.py take dset1 and dset2 arguments and align dset2to1 and child epi commands? I have found those arguments work well as a stand alone align_epi_anat.py script - but I can't seem to get them built into afni.proc.py.
I want to align anat to anat and child epi within afni.proc.py on a se
by
PeterK
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AFNI Message Board
I would like to take my 8run (8 row) timing files and split them up into 8 individual .1D files (because I want to run 3ddeconvolve on each run separately - is there another way to do this??).
It sounds like I can do this with timing tool? Perhaps I have the format of my partitions file wrong?
Should the partitions file have the names of the new timing files, each name on each row?
like
by
PeterK
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AFNI Message Board
Does anyone have experience running 2dwarper?
Do you know what these errors mean?
Thanks, Peter
*+ WARNING: !! Consider using program 3dQwarp instead of 3dAllineate -nwarp !!
** FATAL ERROR: Can't compute autoweight: max value seen as 0
** Program compile date = Dec 5 2013
Replacing Faulty Slice 0041 at time index 0411
*+ WARNING: !! Consider using program 3dQwarp instead
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PeterK
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AFNI Message Board
Ok, Thanks Daniel.
But @2dwarper.Allin also changed my -epan into -fbuc.
Should I be concerned about this??
I suppose 3drefit will take care of thsi but, thought I should ask anyway.
Peter
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PeterK
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AFNI Message Board
It appears that @2dwarper is dropping obliquity information. Also, why is it changing my -epan into a -fbuc?
ORIGINAL DATA
++ 3dinfo: AFNI version=AFNI_2011_12_21_1014 (Dec 5 2013) [64-bit]
Dataset File: dp9t_131205_EPI_E17+orig
Identifier Code: XYZ_upzkllR9c66VAnc5W8IgCw Creation Date: Thu Dec 5 15:50:15 2013
Template Space: ORIG
Dataset Type: Echo Planar (-epan)
Byte Or
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PeterK
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AFNI Message Board
I should have stated, my subjects have large temporal lobe muscles, and I think I'll need to do 2dwarper on skullstriped EPIs, which is why I was asking when in the preprocessing stages I can use 2dwarper.
I'd like to test it this way:
place correction, tshift, deoblique, skullstrip, then 2dwarper. Is this order of events discouraged?
Thanks again, Peter
by
PeterK
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AFNI Message Board
Hi All,
I would like to try 2dwarper.Allin on my data. I suspect some recent sessions contain more motion artifact than usual; the shimming changes when the animal moves and the base of the brain appears to shift up.
At what point in the preprocessing should I use 2dwarper?
Before or after tshift and deoblique??
I am getting the error "ver: Undefined variable." But I am upd
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PeterK
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AFNI Message Board
Ok, thanks for the advice! Yes, I can easily edit my timing files and try it that way -- with the regress motion per run.
by
PeterK
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AFNI Message Board
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