Show all posts by user
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
Page 1 of 1 Pages: 1
Results 1 - 28 of 28
The Pediatric Mood and Anxiety Disorders Program (P-MAP) at the Icahn School of Medicine at Mount Sinai (ISMMS) is seeking a highly motivated post-doctoral scholar in neuroimaging. The focus of this position will be on analyzing fMRI and/or MRS data.
Candidates should have (or nearing completion of) a Ph.D. in neuroscience, psychology, cognitive science, radiology, or related field and have a
by
dewitt.77
-
AFNI Message Board
Thanks for the response, Rick. If I try to run the command to remove AFNI, I'm given the following Error E: Could not get lock /var/lib/dpkg/lock -open (11:Resource temprarily unavailable)
E: Unable to lock the administration directory (/var/lib/dpkg/), is another process using it?
When I navigate to that file directory, the lock document cannot be opened, it says I do not have the perm
by
dewitt.77
-
AFNI Message Board
Hi Rick,
I want to check if there is a different package I should try updating, or re-installing, based on the output information I sent in my last response. It seems Debian weezy/sid was what was installed previously. As I said, AFNI will still open when called in the terminal, but 1. None of my commands will run in the terminal and 2. Even restoring back to what I had originally, is an outd
by
dewitt.77
-
AFNI Message Board
It seems you're right. afni-ver returns the following
Precompiled binary Debian=x86_64-1-gnu: June 12 2017 (Version-16.2.07~dfsg.1-5~nd12.04+1
I'm not sure to what the June 12 2017 refers. When my afni commands were still working, I verified that the 3dclustsim being run by my current installed AFNI was from 2014(hence my need for an updated version for the new 2015 add ons). Th
by
dewitt.77
-
AFNI Message Board
Hi Rick,
Thanks for the quick response! In a new terminal, yes my commands like ls and @update.afni.binaries are recognized. However, if I attempt to run a specific package, or even defaults with the @update.afni.binaries I get an error which says I do not have write permissions in the install directory (install dir = /usr/bin), my IT dept has told me they do not have admin control over this s
by
dewitt.77
-
AFNI Message Board
Hello,
I was attempting to do an AFNI update in order to gain access to some newer options (specifically the ACF method of 3dClustsim). The @update.afni.binaries command could not be recognized on my Ubuntu 12.04 system. So I was attempting a manual update by downloading the linux.ubuntu_16_64.tgz package. This however, was stopped part of the way through as it could not recognize the direc
by
dewitt.77
-
AFNI Message Board
Thank you for the responses! My confusion ended up being related to the coarseness of my grid. I did have a follow up related questions however.
1. What exactly dictates the percentage of voxels from a mask out of total voxels which are used for the simulation in 3dClustSim? I ask because typically I use an mean anatomical mask, the same used in 3dfim+ when generating my zmasks, which has bee
by
dewitt.77
-
AFNI Message Board
Hi, thank you for the response. No I'm attempting a 3D sphere with a radius of 4mm. Trying the 2D circle option with linear fill-in with circles instead of spheres reduced the number of surviving voxels further actually (to 13). The way I've drawn this ROI is by taking anatomical mask that has been resampled to the grid/voxel size of my functional images, I'm wondering if there i
by
dewitt.77
-
AFNI Message Board
As a follow up/adjoining question: I was a little perplexed as to the small number of overall voxels being interrogated in my 3dClustSim across all my ROIs. To generate my ROIs I used the draw dataset function in the AFNI gui. I generated a 3D sphere, with a radius of 4mm, linear fill in: A-P, gap: 2mm (my voxel size). However, when I do 3dROIstats, or 3dMaskave even, the number of voxels in
by
dewitt.77
-
AFNI Message Board
Hi Gang, thank you for the response. I calculated the voxel-wise connectivity between a seed region and those 12 ROIs. Voxel-wise based on my understanding of 3dfim+. And Each ROI had 33 voxels, so my 3dclustSim was run on 396 voxels total (12 x 33). The commands I ran are below (in this code, Striatal_Seed_Mask contains the 12 ROIs, left sgACC is the seed).
The 3dClustSim with my ROI
by
dewitt.77
-
AFNI Message Board
Hello,
I’ve read in the 3dclustSim help output the issue that can arise from trying to find a cluster size for a given with small ROI masks, p, alpha combination. I'm wondering though, what AFNI users do to circumvent this issue? In SPM I know pit is typical to apply RFT with a certain z score cut off. But I haven't been able to find how one might go about that in AFNI. The con
by
dewitt.77
-
AFNI Message Board
Hi Daniel,
This is a really helpful tool, thanks! I wanted to clarify the L/R issue when using AFNI as it has been a while since I've used it. My understanding is that the standard convention with the AFNI image viewer is left= right, and you can do a mirror flip, but this really only adjusts for viewing purposes only, regions displayed on the right in left=right view for example will sti
by
dewitt.77
-
AFNI Message Board
Hello,
I am having an issue when viewing my results in AFNI where both the whereami and "go to atlas location" functions are unavailable. when I right click, they are there but they are unhighlighted and unable to be clicked on. My results, and anatomical underlay are in MNI space, but I've never had this be an issue before. My understanding is that regardless of your individual
by
dewitt.77
-
AFNI Message Board
Thanks, Rick! This makes sense. The resting state data I'm working on I inherited and it was pre-processed using CPAC rather than the typical afni_proc.py..The same processing steps were followed though. Is there an command to get the epits output that I can apply to my processed data? Thank you!
Sam
by
dewitt.77
-
AFNI Message Board
Hello AFNI experts,
I'm attempting to ascertain the appropriate cluster threshold for FWE via 3dClustSim for a resting state analysis I'm performing. In the past, with task data, I have always used a residual error input data set for my 3dClustSim based on the rationale that I want to make my estimation based on an input that does not inherently model my design/anatomy(i.e. something
by
dewitt.77
-
AFNI Message Board
Thanks, Rick. I think the issue might be that I don't have the residual masked. Whenever I've used 3dClustSim previously it has been on images that are already masked and/or censored. The reasoning for using the residual image however was so that the image does not have an anatomical structure, rather, the structure of the noise..If I mask it with, say a whole brain mask, or something s
by
dewitt.77
-
AFNI Message Board
Hi Gang,
Thank you for the response! From what I can tell these residuals are indeed timecourse at each voxel. As for the smoothing kernal info..when you look at the contrast image, it gives you FWHM info, for example my contrast image gives the following.. 12.5 12.5 12.2 mm 6.3 6.3 6.1..read as, original smoothing kernal being 6mm and effective smoothing is 12.5..etc. in the xyz direction.
by
dewitt.77
-
AFNI Message Board
Hello,
I'm attempting to account for inherent smoothing in order to determine appropriate cluster thresholds. I'm using 3dFWHMx for this. In the past I've used this directly on the images which go into my analyses, but I've since been told that you want to use a dataset that is the structure of the noise rather than the anatomy, and for this reason, residual images are bes
by
dewitt.77
-
AFNI Message Board
Thanks, for the response! I see what you mean about individual subject variation. The reason for using a gray matter mask at the single subject stage is out of a necessity for the average time signal I extract per ROI per person to come specifically from gray matter. The end result of this analysis is outcome measures from the Brain Connectivity Toolbox, which involves inputting connectivity mat
by
dewitt.77
-
AFNI Message Board
Thank you! This appeared to fix that issue. In terms of the quickest way to create a gray matter mask, what is the easiest option. I've read elsewhere that the gyrusfinder plug-in is useful for this. It's unclear to me if when using this you would simply input 0 for the fill of all white matter, and it also doesn't seem to have an option for masking out csf. Thank you!
Best,
Sa
by
dewitt.77
-
AFNI Message Board
Hello,
I'm attempting to use 3dmaskave with an ROI mask I've created applied to my resting state data as shown here
3dmaskave -mask TeenPower_mask+tlrc -mrange 75 75 \
-quiet "$s"_rest-mni-rv.nii > TeenBrain_2.1D
However, the resting dataset i'm inputting does not have white matter/CSF masked out and I am attempting to do so. There are several ways it seem
by
dewitt.77
-
AFNI Message Board
I am also curious about the potential problems that could come up at applying the mask at different stages. In my current pipeline a gray matter mask is generated from the functional dataset after slice-timing correction and volume registration. However, for example I've performed scrubbing techniques on the fully preprocessed images and would like to apply the mask to that. Similar questi
by
dewitt.77
-
AFNI Message Board
Thanks, Rick! This makes sense. My main issue is that I want to group these two data sets together(one is an older group, one younger), and use age as a continuous variable while looking at the patterns within these voxels. But If the output of the mask for one group is this different from the other, that is obviously problematic. But If i'm understanding you correctly, at the very least..if
by
dewitt.77
-
AFNI Message Board
Hello Rick,
Thank you for your reply! Below is a portion of my script, I use 3dmaskave to extract the average timeseries from a mask I created, TeenBrain, that has roughly 180 nodes(ROIs). As I said, when used previously, the output would tell me that 19 voxels survived for each dynamic and would write the average time series parameter estimate to a 1D file, as instructed. With the new data,
by
dewitt.77
-
AFNI Message Board
Hello,
When using 3dmaskave across different data sets which have the same sized voxels, and no specific threshold, I expected the number of voxels per ROI which survived to be the same, and that isn't turning out to be the case. I'm trying to figure out if this is a systematic problem or not. For example, I created a mask with several ROIs, all the exact same size and on one group
by
dewitt.77
-
AFNI Message Board
Hello,
Recently I created an ROI mask that had several ROIs within it, 264 to be exact. I've incorporated this seed into a script I have which extracts time series for a given seed and generates correlation maps which are transformed to z maps. The script runs fine when the file indicated for the ROI has just 1 ROI, but when I put in my file that has multiple ROIs it will run but appear
by
dewitt.77
-
AFNI Message Board