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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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Pages: 123
Results 31 - 60 of 61
Thanks Gang.
I assume, then, that the space is MNI but just the header information is wrong? Can you confirm that I don't need to transform from talaraich to MNI then?
by
swijeakumar
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AFNI Message Board
Ok so firstly, to recap on the previous issue, we tried out both options 1 and 2 for trying out stim files and stim time files and they work now and we get the same results across both. We also compared the idea_reg.1D files and we get the same numbers, but just in case, here are the scripts for both. Can you check them both and let us know if this looks good. Likely should be as the numbers matc
by
swijeakumar
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AFNI Message Board
Hi all
I ran some input files that are in MNI space through 3dMVM and expected to see that my output was in MNI space (checked with 3dinfo -space) too, but it turns out it is in talaraich space. I am not sure why this has happened. I updated my version of AFNI and still get the same results.
I think I could convert it to MNI space but I just want to make sure there isn't anything I am
by
swijeakumar
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AFNI Message Board
It did not make a script - seemed to have stopped before that. I can send you the error message in a bit.
Can I double-check on one thing on a separate model: When I am running a GLM model with only stim files (and no sim times) that don't need convolution because it has already been taken care of, can I just use regress_stim_file in the GLM? I forgot to delete the basis function line so
by
swijeakumar
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AFNI Message Board
Here's what we tried based on option 1, and it seems to be running so far. Can you check to confirm this is what you meant?
afni_proc.py -subj_id $i \
-dsets $run1 $run2 $run3 $run4 $run5 \
-do_block align tlrc \
-copy_anat $t1 \
-volreg_align_to last
by
swijeakumar
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AFNI Message Board
Whoops. Apologies, there's en error in what I wrote before. I was meaning to ask whether regress_stim_files and regress_stim_times can be used together (not labels!). I know we have run this in the past without problems but now I am unable to. Could it be because I made an update?
Under -regress_stim_files option:
The user must specify either -regress_stim_times or -regre
by
swijeakumar
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AFNI Message Board
Hi all
Is it possible to use both regress_stim_labels and regress_stim_files in the same afni_proc file? We were able to do this a few weeks ago but since an update to AFNI, are unable to. The documentation also says that we can't.
Any advise is appreciated.
Thanks!
by
swijeakumar
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AFNI Message Board
Sorry about the late reply.
We upgraded afni and re-ran 3dMVM and the output still says TLRC when we check with 3dinfo.
Any advice?
by
swijeakumar
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AFNI Message Board
Hi there
I have a question that I am trying to find an answer to online, but have had no luck yet.
Basically, I have a correlation map (nifty format) and I want to find the euclidean distance (or as number of voxels) between a voxel that has the highest correlation value and from a projection point vertically above on the surface of the brain. I am trying to determine how deep the best corr
by
swijeakumar
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AFNI Message Board
Here is my output:
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 14.1.0
version: Darwin Kernel Version 14.1.0: Mon Dec 22 23:10:38 PST 2014; root:xnu-2782.10.72~2/RELEASE_X86_64
distribution: 10.10.2 x86_64
number of CPUs: 4
apparent login shell: bash
by
swijeakumar
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AFNI Message Board
Some extra info : my input datasets are nifti files in MNI space.
by
swijeakumar
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AFNI Message Board
My input data is in MNI space (checked with 3dinfo) and I also used 3dinfo to check the space of my output and it says tlrc. Further, +tlrc is attached to the output (I know that doesn't really mean much). Not sure whats going on.
by
swijeakumar
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AFNI Message Board
Hi there
I have a Q about 3dMVM.
Is it the case that results from 3dMVM is in talairach space always?
Thanks.
S
by
swijeakumar
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AFNI Message Board
Hi Rick
Sorry for the late reply.
Well, when I ran 3dinfo -space on the input data going into 3dMVM, that was in MNI space and then the output ANOVA result is in tlr. space. I am not sure what is going on..
S
by
swijeakumar
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AFNI Message Board
Hi all
I ran 3dMVM on datasets that were converted to MNI space using 3dAllineate. After running 3dMVM, my ANOVA result was in tlr. space. I needed to convert it back to MNI space so I used 3dWarp:
3dWarp -tta2mni -prefix MNI_MRI_3dclust_Acc MRI_3dclust_Acc+tlrc
It worked and when I looked up the space using 3dinfo, it says MNI - which is what I want, but I am confused as to why it stil
by
swijeakumar
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AFNI Message Board
Hi all
I had a question about censoring a volume that had missing slices. Here's what I had in mind:
1. I replace the volume with missing slices with the previous volume (a duplication basically).
2. I am using afni_proc and so the best option I have for censoring is regress_censor_extern, correct? In my case, each subject has 5 runs and really, only the 2nd run of one subject has tha
by
swijeakumar
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AFNI Message Board
Hi all
I seem to have an issue with sorting and running to3d on a couple of runs from a couple of subjects in the dataset. Upon closer inspection it looks like, some of the volumes of each of those runs (for e.g.. in one of those subjects) have different number of slices (31 and 33 slices), so to3d complains of the total number of slices being different. Does anyone have a solution for this?
by
swijeakumar
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AFNI Message Board
Hi there
I added a mask option to my otherwise completely functional 3dMVM function and it produces an error :
** Error:
Quitting due to model test failure...
Does the position of the mask option in the command matter? I didn't think it did, judging from the examples I saw on the message board. I have attached my ROI - it is an IFG ROI and it has the same smoothing parameters a
by
swijeakumar
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AFNI Message Board
Hi all
How do I calculate the residual variance as a result of an individual-based Deconvolution (3dDeconvolve). the file obtained from using the -errts option provides the residual variance as a function of time, correct? So would I just average?
Thanks
S
by
swijeakumar
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AFNI Message Board
Apologies. Could not attach paper: Here's the title:
A simple solution for model comparison in bold imaging : the special case of reward prediction error and reward outcomes
by
swijeakumar
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AFNI Message Board
Hi all
I have question about multicollinearity issues.
I have data from 10 subjects and 3 runs each. There are 12 regressors (two types of trials x hit or misses x 3 stages in a trial). 1dplot.py on the xmat design matrix tells me that the last two stages of each trial are correlated (>0.7). I used 3dDeconvolve.
If I was interested in closely examining the contributions of these two r
by
swijeakumar
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AFNI Message Board
FYI, this is what the terminal window displays and stops at :
Loading required package: phia
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (Jan 15 2014) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset Prop_ANOVA+tlrc
+ created 8 FDR curves in dataset header
++ 3drefit processed 1 datasets
by
swijeakumar
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AFNI Message Board
Hi all
I have tried to use 3dMVM to do a 3x2x2 ANOVA. I have attached my code below. It appeared to have worked, in that it creates the main effects and interaction effects. But I would like to double check that I have gone through this correctly:
1. I used the beta coefficients for each regressor that afni_proc gave me as the input to -dataTable. Does this sound legit?
2. Am I right in as
by
swijeakumar
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AFNI Message Board
Hi all
I have a question about using GroupAna. Such is my design : 20 subjects performed two tasks (Task A and Task B). Each Task had 3 runs each (each run being a Load condition : Load 1, Load 2 and Load 3). Each Load (and Task) had two types of types of responses (Type A and Type B).
So basically, I have 4 factors : Task (2 levels), Load (3 levels), Type (2 levels) and Subjects (20 level
by
swijeakumar
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AFNI Message Board
Just to make sure I am on the same page, what is the accepted method of Group analysis on the whole brain level using 3dANOVA3. Are they such :
1. Run 3dANOVA3 with main effects (-fa, -fb options), interactions (-fab option) and contrasts (-Abcont, aBcont etc.)
2. Check the main effects and interactions to see if they have reached singifcance. Do I do this with the cluster size I get from 3dc
by
swijeakumar
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AFNI Message Board
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Pages: 123