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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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Results 61 - 90 of 128
Bob,
Thank you very much for this! Your suggestion offers an interesting way to portray color with transparency. But it also appears that we can not try transparency for a diverging color palette (eg blue through white to red) which might be useful if we want to highlight negative to positive values of contrast test statistics. Is that not possible?
Thanks again!
Best wishes,
Ranjan
by
maitra
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AFNI Message Board
Hi Brian,
Thanks! Sorry but this does not make a difference. (This is not surprising because I do not keep cache.)
Many thanks and best wishes,
Ranjan
by
maitra
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AFNI Message Board
Hello,
I am on Fedora 23 using Firefox 45 but this is true of any browser used on Fedora 23 at Iowa State University.
I am unable to get to the AFNI message board. I can only get to the http version but that is not usable at all. Certainly, I can not log in and it is hard to read the messages now.
Here is the error message I get:
Quote
Secure Connection Failed
An error occurred du
by
maitra
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AFNI Message Board
Hi,
I think I know how to add my own palette in AFNI. I was wondering how to include a palette which has different amounts of transparency. In particular, my palette has higher opacity (alpha) values for higher values of the test statistic.
Is there a way to add this in, in addition to the RGB palette?
Many thanks in advance for your help in answering this question!
Best wishes,
Ran
by
maitra
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AFNI Message Board
Bob,
Thank you very much! I did an analysis on several brains using uber_subject.py in AFNI on a dataset. I believe that all the brains were Talaraiched and then analyzed. Would this information be in the directory somewhere? (There is no directory called Segsy).
Alternatively, what should I be applying the 3dSeg to? To the registered anatomical sequence?
Apologies: I am a statisticia
by
maitra
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AFNI Message Board
Dear friends,
I am reading this paper:
Citation: Wang Y, Li T-Q (2013) Analysis of Whole-Brain Resting-State fMRI Data Using Hierarchical Clustering Approach. PLoS ONE 8(10): e76315. doi:10.1371/journal.pone.0076315
where, as per the authors:
"individual datasets were masked with a standard gray matter template derived from FSL tissue priors (http://www.fmrib.ox.ac.uk/fsl) to exc
by
maitra
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AFNI Message Board
Rick,
Sorry to revisit this again, but what does the pb03.Imag_anat2epi.r01.volreg+tlrc contain? Is it the blurred data? Btw, how is the blurring done in the pre-processing data step?
Many thanks and best wishes,
Ranjan
by
maitra
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AFNI Message Board
Rick,
Thanks! Is the first command enough to update SUMA also? Or is something addiitional also needed?
Many thanks,
Ranjan
by
maitra
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AFNI Message Board
Thank you! I am on a slow connection this week so will have to wait to get back before proceeding (bummer!). It would be nice to have (at least an unofficial) rpm so that updates can be automatic from a repository but that might be a lot of work to get going.
by
maitra
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AFNI Message Board
Hi,
I have been having this issue with Fedora 23 in that when I start up SUMA, all is well till I click on Object Controller. Then SUMA (but not AFNI) comes crashing down with the following message:
$ suma -spec N27_rh.spec -sv MNI_N27+tlrc.
Quote
$ ++ Environment variable = already set to 'SUMA_SUMA_TESSCON_AutoScale'. Value of 'SUMA_CountProcs_Verb' from /home/maitra
by
maitra
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AFNI Message Board
Dear friends,
I have an anatomic image and a segmented image (from resting state functional image data). Both are in NIfTI format. The latter image has segments marked by 0 (which I am not interested in displaying), 1, 2, 3, 4 and 5. I want to display these segments showing the different kinds of activity using AFNI/SUMA. Do you have suggestions as to how I should go about it? I tried putting
by
maitra
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AFNI Message Board
Hi, Thanks for pointing me to 3dresample: that really is an easy way out.
Best wishes,
Ranjan
by
maitra
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AFNI Message Board
Hi,
I am trying my luck with learning to use AFNI to postprocess and accquire resting state data (for further analysis and methodological developent using C and R codes) and I think I got things to work. My question is: is it possible to get the registered anatomical data (of the same volume dimensions) as the registered, normalized, etc. EPI image for the resting data. Here is a list of files
by
maitra
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AFNI Message Board
Hi,
This is not a question on AFNI but I thought that this was a good place to get some insight into.
I came across this question after looking at the source code for simuating artificial datasets from software such as neuRosim (in R). Here, datasets are simulated from a fMRI time series using a given design matrix and SNR. My question has to do with this SNR calculation. From what i see of
by
maitra
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AFNI Message Board
Thanks! I actually know of this paper: this is very helpful!!
Best wishes,
Ranjan
by
maitra
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AFNI Message Board
Hi,
Sorry, but does anyone know the answer to this question? I would like to make the correct references.
Thanks,
Ranjan
by
maitra
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AFNI Message Board
Hi,
I am writing about 3dClustSim performed by AFNI in a manuscript for publication and I was wondering what is the correct references for the methodology behind this algorithm. I am not asking for the reference to AFNI, rather the reference to the methodological work behind 3dClustSim.
Many thanks,
Ranjan
by
maitra
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AFNI Message Board
Thanks very much! Yes, you are correct, I am in the learning stages. Thank you for pointing out the link.
Best wishes,
Ranjan
by
maitra
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AFNI Message Board
Thanks, Ziad!
But hmmm.....I do not have a colormap with my SUMA. All I have is the window on which the mapping happens (and can be rotated with the mouse).
Many thanks,
Ranjan
by
maitra
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AFNI Message Board
Hi,
Is it possible to print the colormap from AFNI/SUMA into a separate jpg, etc file?
Thanks,
Ranjan
by
maitra
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AFNI Message Board
Thanks! What i was able to do is use ctrl-r and then this creates an autorecord* file. This I converted to eps using ImageMagick.
Best wishes,
Ranjan
by
maitra
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AFNI Message Board
Hi,
I have a strange problem. I get suma working and then I press "r" a window (titled snapshot) appears. I then press shift-D and I get a window which has, among other options, "save to .eps(s)" and I check it and press done. The window goes away but nothing shows up in any directory from what I can tell. Where is this file produced?
Many thanks,
Ranjan
by
maitra
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AFNI Message Board
Thanks! I cited Cox (1996) and also several others (Cox, 2012; Saad et al, 2009; Saad and Reynolds, 2012, etc) but I was wondering if there was an official citaton. I guess not. I will add Cox and Hyde (1997) to the list.
Thanks again!
by
maitra
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AFNI Message Board
Hi,
Could someone please tell me how to cite AFNI (ie provide the bibliographic reference) in a publication?
Many thanks,
Ranjan
by
maitra
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AFNI Message Board
Gang,
Thanks!! I did use -Rbuck. Where would this information be stored, and how do I extract this? The following is the command used:
3dREMLfit -matrix X.xmat.1D -input pb04.Imagination001.r01.scale+orig.HEAD \
-fout -tout -Rbuck stats.Imagination001_REML -Rvar stats.Imagination001_REMLvar \
-Rfitts fitts.Imagination001_REML -Rerrts errts.Imagination001_REML -verb $*
Many thanks agai
by
maitra
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AFNI Message Board
Hi,
I ran 3dREMLfit using the proc_afni.py script:
3dREMLfit -matrix X.xmat.1D -input pb04.Imagination001.r01.scale+orig.HEAD \
-fout -tout -Rbuck stats.Imagination001_REML -Rvar stats.Imagination001_REMLvar \
-Rfitts fitts.Imagination001_REML -Rerrts errts.Imagination001_REML -verb $*
Now, I want to know if it is possible to get the value of the (usually uninteresting term) intercept
by
maitra
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AFNI Message Board
Sorry to bring this up again, but is there a paper reference for this dataset, i.e. where it was analyzed/published. I understand that it is part of a bigger group study, but I would lke to include the reference if I use the dataset (which I am hoping is ok to do).
Many thanks and best wishes,
Ranjan
by
maitra
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AFNI Message Board
Hi,
How does one save the background in a SUMA image to transparent? I can not seem to change the black background to anything else -- it would greatly help in saving ink.
Many thanks and best wishes,
Ranjan
by
maitra
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AFNI Message Board
Hello,
Sorry if this question has been asked and answered before, but I could not find it on a search this afternoon. (I did hunt around a fair bit, but I am pretty bad at online searching.)
Anyway, I have been using the data6 to learn about AFNI. I presume that this dataset is in the public domain and can be used in publications? I was wondering what publication(s) beyond the AFNI softwa
by
maitra
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AFNI Message Board
Hi Rick,
Thanks very much! I see now. Btw, we hae done some AR(p) processing (to go above the ARMA(1, 1) currently available in AFNI). Is this of interest to the developers? This is in C code.Perhaps we will do ARMA(p, q) later.
We tried it on the false beliefs dataset available on openfmri.org and got an AR(2) model.
Many thanks and best wishes,
Ranjan
by
maitra
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AFNI Message Board
Page 3 of 5
Pages: 12345