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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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Dear AFNI developers,
Kind of an odd question, but.... I often need to open datasets sitting in remote servers: I ssh into the server with X11 forwarding, start afni there and try to work this way, but it can be very slow due to the heavy message passing of the graphical interface through ssh. Is there is a way to use the local afni machinery, that is, starting afni locally and just open a r
by
gpagnon
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AFNI Message Board
Hello Gang,
thanks for the swift reply and yes, I can see the issues you pointed out with the conventional approach. I had actually printed out your paper a while ago, but hadn't been able to read it yet: this gives me the right priority to do it.
hope to see you at the next HBM
giuseppe
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gpagnon
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AFNI Message Board
Hi all (and especially Gang ,
I know this has been discussed before, and there were also some notes about it on Gang's page (which do not seem to exist anymore), but I wonder what is the current preferred method in afni land for detecting regions that are significantly activated by two contrasts --- (cond.A - cond.B) and (cond.C - cond.D) --- and whose levels of activation are *not* signi
by
gpagnon
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AFNI Message Board
Hello Paul
Got it, and yes, I do agree with the approach of thresholding with t-value but displaying the beta or contrast values. Thank you also for sending the links!
very best
giuseppe
by
gpagnon
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AFNI Message Board
Hello,
thank you for your reply, it does make sense. I'll have to say, though, that when I am looking at t-maps and threshold them, the clusters have a much better "graded" appearance if I manually set the range at the max abs t-value, while if I choose the default autorange I get solid red (and/or blue) clusters.
Also, one last thing, just to clarify: in the first (yello
by
gpagnon
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AFNI Message Board
Hi all,
not a big deal, but it seems that the autorange function for the colorbar doesn't not function properly anymore. For instance, if I have:
Thresh range: -5.37 : 18.53
Setting the autorange box, I get the value: 2.69 (with percent box unchecked)
I remember the autorange setting the value to the max abs of Thresh range, has this behavior changed?
I am running version
by
gpagnon
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AFNI Message Board
Hi Daniel,
thanks for your reply, I see. The sizes of the pmaps files are quite small though (a few mb), so it may be worthwhile to keep them in the distribution unless their usefulness/accuracy has not stood the test of time.
best
giuseppe
by
gpagnon
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AFNI Message Board
Hi all,
a quick question. When using the "WhereAmI" button in the clusterize report window, I get the following warning messages in the terminal:
** Warning: Atlas CA_N27_PM could not be loaded.
** Warning: Atlas CA_PM_18_MNIA could not be loaded.
** Warning: Atlas DKD_Desai_PM could not be loaded.
** Warning: Atlas DD_Desai_PM could not be loaded.
** Warning: Atlas FS_Desai_
by
gpagnon
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AFNI Message Board
Hello,
I am encountering a strange issue while reconstructing a T1-weighted image from a 3T GE scanner, especially since I have been processing other subjects with exactly the same protocol and had no problem. Here is the command I used and its output:
Dimon -infile_prefix MR -gert_create_dataset -save_details DET
Dimon version 4.26 (February 3, 2020) running, use <ctrl-c> to qui
by
gpagnon
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AFNI Message Board
Hi all,
I am not sure about the slice acquisition order of some EPI sequences from a GE Architect Signal 3T scanner. Does anybody know if there is a way to extract this information from the dicom files (eg, through dicom_hdr)? I tried but I couldn't find any of the tags that were suggested on the web as potentially carrying that information. I do know that the sequence was interleaved,
by
gpagnon
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AFNI Message Board
Hi Justin,
good to hear from you! Thank you for your quick reply and sorry for my late one . I just reinstalled AFNI from scratch today using the latest build and your instructions, and it seems to work well so far. I wonder if it may even work with R 4.0.2.
hope everything's well
giuseppe
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gpagnon
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AFNI Message Board
Hi all,
I am trying to install AFNI on a new MacBook Pro running Catalina. I followed the instructions except that I avoided homebrew (I use macports) and kept R 4 instead of R 3.6. I know that AFNI is not compatible with the newer version of R and that's fine for the moment (I haven't yet decided whether to roll back R to the previous version, because of other constraint). On thi
by
gpagnon
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AFNI Message Board
Hi Rick,
Alright, I see ... if you check the "Pos?" box under the colorbar in the main AFNI window, in the Cluster Results window the 4th line from the top ("Alpha -> Cluster Thresh") gives cluster size thresholds that match indeed the values in the clustsim*1sided.1D file saved by 3dttest++ (with the option -Clustsim).
If you leave the option "Pos?" unche
by
gpagnon
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AFNI Message Board
Hi,
a quick question here. What is the thresholding scheme (1-sided, 2-sided, bi-sided) used for displaying the alpha values in the Cluster Results window? Given the rationale in the 3dClustSim help text, I would think it's the 2-sided one, but I just wanted to make sure.
Perhaps I should also add that I am examining a Z-map obtained from 3dttest++ with the new option "-Clustsi
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gpagnon
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AFNI Message Board
Hello Daniel,
(in my last post I wrote Glen, but I meant Dan! blame it on the euphony
grazie mille a te, for the instant fix!
best
giuseppe
by
gpagnon
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AFNI Message Board
Hello (Glen?)
In trying to convert a dataset from TTA to MNI, it seems that the option -newgrid does not actually change the voxel size of the output dataset (with respect to the input dataset), using the command
3dWarp -tta2mni -newgrid 2 -prefix data_mni data_tta+tlrc
Is there any special caveat to the usage of the option that I am not aware of?
thanks for any comments!
giuseppe
by
gpagnon
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AFNI Message Board
I have actually found this message thread:
which provides some useful information. I guess I don't need a reply then, if things haven't change since then
by
gpagnon
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AFNI Message Board
Dear AFNI experts,
I have previously run a dataset through the afni_proc.py pipeline, with affine TT spatial normalization.
For a new collaboration project based on these data, I need to convert all the pre-GLM data to MNI space (EPI+T1). Could anyone point me to the quickest/best way to do it (I have 45 subjects, with 6 EPI runs per subject)?
More specifically, would you advise to Qwa
by
gpagnon
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AFNI Message Board
Hello Gang,
very good points you are making there, and I hadn't thought at all about the effect of the historical trend of increasing sample sizes on the employed statistical strategy: with the number of subjects in a study reaching sometimes the three digits, the problem of "too much" activation becomes more and more real, and a sort of "rich-world" curse!
Your id
by
gpagnon
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AFNI Message Board
Hello Gang,
thanks for your thoughts, those are good points to ponder. In fact, when I want to get more spatially-specific information about the activations, I tend to raise the statistical threshold until I get reasonably spatially-restricted clusters. However, it just happens sometimes that, in the same study, you have some contrasts that look good at a reasonable threshold of, say, p=0.00
by
gpagnon
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AFNI Message Board
Dear all,
the suggested way to do a conjunction analysis in AFNI, in order to identify the brain areas that are commonly activated by two different conditions (or better, contrasts), is to compute the spatial intersection of the statistically thresholded maps corresponding to the two selected conditions/contrasts.
However, since those maps are typically thresholded using a combination of
by
gpagnon
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AFNI Message Board
Thanks to Bob and all the AFNI group for the tremendous support and advice on this forum and for developing the only software I know that is actually FUN to use: happy anniversary!!
giuseppe
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gpagnon
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AFNI Message Board
Dear all
sorry, but I seem to keep stumbling on orientation issues these days!
Using 3dmaxima on an RPI-oriented tlrc dataset (in MNI template space), I get exactly the same output with and without the flag "-dset_coords", even though the output reports "RPI mm coordinates" when using the flag and "RAI mm coordinates" when not.
Does this have to do with the
by
gpagnon
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AFNI Message Board
Dear all,
I am trying to get the atlas locations of a set of clusters. The dataset is a tlrc dataset in MNI space (volumes were spatially normalized in SPM, and the header was refitted to incorporate the information about being in MNI space). If I right-click a location in the viewer and choose "whereami", I get the usual list of anatomical locations according to the atlases. Howeve
by
gpagnon
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AFNI Message Board