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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: 12
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I see that AFNI is available on Mac OS X, but I don’t see an IOS version. I have a IPad Pro and would like to download AFNI so I can mask lesions and draw ROI’s with my Apple Pencil. Is there a version that will work on the iPad?
Thanks!
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Dxc536
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AFNI Message Board
oooh, thanks! I was confused what C level meant. I assumed a level would group them into their 'groups' where c level signified if it was independent or a paired test (i.e. like values means same participant)
It works with your suggestion.
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Dxc536
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AFNI Message Board
Hello,
I have a 2-way mixed design (2 conditions at 2 time points)
I keep receiving the following error:
++ 3dANOVA3: AFNI version=AFNI_19.2.10 (Aug 7 2019) [64-bit]
++ Authored by: B. Douglas Ward
** FATAL ERROR: Program 3dANOVA3: must have equal sample sizes for 3dANOVA3
** Program compile date = Aug 7 2019
when I run:
#!/bin/bash
Bank=4
echo $Bank
3dANOVA3 -type 4
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Dxc536
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AFNI Message Board
Here's a hypothetical situation and please let me know if I'm thinking about it the wrong way:
Say I'm running group stats on the T-Statistical map. For one group the Average T-Stat for a cluster is 0.5 and for the other group the average T-stat for the cluster is 1.5 (very little variance). Wouldn't that cluster be considered significant despite either cluster reaching a p
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Dxc536
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AFNI Message Board
Hello,
I would like to run 3dttest++ and perform a 1-sample test. I might be missing it in the notes, but is there a way to indicate the single subject Pthr to run through group level analysis? That is, only include voxels that are significant at the single level in the group level analysis?
The only way I can think to do this is to save the 3dclusterize map (-pref_dat) to extract the sign
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Dxc536
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AFNI Message Board
Hi Rick,
I'm working on the same dataset. All of the Afni_Proc.py (which is run on individual subjects) output is in participant space.
In parallel to afni_proc.py we use auto_warp.py to nonlinearly warp T1 images to MNI 2009c space. Subsequently, we use 3dNwarpApply (-iwarp) to bring the stats and anything else from patient space (which was epi2anat aligned) to MNI space. Ultimately,
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Dxc536
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AFNI Message Board
Thanks.
How do I use the cluster approach to create the Condition*Time interaction map so that I can then do the post-hoc comparisons using 3dttest within the significant clusters?
by
Dxc536
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AFNI Message Board
Hello,
I have a dataset where I'd like to perform a 2-way repeated measures ANOVA (Condition*TIme). I've been using 3dANOVA3 -type 4 to achieve this, but I was wondering if there is a way to include 3dClustim in a similar way to 3dttest (-Clustim)?
I'm not sure if this is the best approach, but my plan is to use 3dANOVA to generate Condition*TIme interaction maps with the F-s
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Dxc536
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AFNI Message Board
I have always been confused if it's more appropriate to align the epi to the anat and then run the rest of the preprocessing steps on the newly aligned epi file, or to align the ant to the epi and run the preprocessing steps on the original epi file.
Does anyone have advice or can provide a brief reasoning why I shouldn't do one or the other?
This becomes more confusing because I
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Dxc536
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AFNI Message Board
Thanks. I just sent the email. See below for the output:
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 5.4.0-88-generic
version: #99-Ubuntu SMP Thu Sep 23 17:29:00 UTC 2021
distribution: Ubuntu 20.04.1 LTS
number of CPUs: 8
apparent login shell: bash
by
Dxc536
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AFNI Message Board
Hello,
I'm trying to use Cluster Explorer and I keep running into errors.
When I run ClustExp_HistTable.py I get the following error:
Traceback (most recent call last):
File "/home/dxc536/abin/ClustExp_HistTable.py", line 144, in <module>
if not ("3dttest++" in hist_all or "3dMVM" or "3dLME" in hist_all):
TypeError: a bytes-li
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Dxc536
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AFNI Message Board
Thanks, Rick.
From a best practice stand point, why is motion correction relative to the base of 1 run? Is it simply because of alignment issues? Along those lines, if we chose to use an alternative motion correction (e.g. SLOMOCO), is there an option that will align both runs? Does alignment of both runs occur automatically? Or is is this typically done through the volreg options?
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Dxc536
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AFNI Message Board
Hello,
What is the best way to report motion with the 3dvolreg? I'm using -dfile to output the motion parameters, but I don't see how the output corresponds to the output displayed when -maxdisp is used. I'm unable to find the same result displayed in the .txt file created with -dfile. Also, is it possible to report the max displacement and the mean displacement?
Thanks
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Dxc536
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AFNI Message Board
Chronic stroke participants in the study underwent 5 weeks of rehabilitation and the primary objective is to assess pre to post changes in functional connectivity based on severity of impairment. In addition to resting state, participant performed a self-paced finger flexion/extension block paradigm.
The overall goal is to compare connectivity maps between ROI's that were determined base
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Dxc536
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AFNI Message Board
Thanks.
I'm using fMRI in order to establish seeds for resting state. The plan is get the peak beta coefficient in 4 different regions (L/R M1 and PMd), after choosing an appropriate -pthr. Do you recommend another approach if clusterzing is typically done on the group level or is it okay to run it on individual subjects?
Would it be better to just use the peak t-stat?
by
Dxc536
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AFNI Message Board
Hello,
Is there a way to call the ClustSim.ACF*.1D file when using 3dClusterize? Specifically to input the appropriate -clust_nvox for the corresponding p-value, NN and 2sided?
I would like to bash 3dClusterize on a number of different subjects and would like to automatically use each corresponding -clust_nvox located in the /*.results/files_ClustSim folder. Or is it advised to just use the
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Dxc536
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AFNI Message Board
Thanks.
The output is 11101. The 0 means they are not on the same grid, right? When I resampled to one of the EPI's then they are on the same grid (11111).
I checked the original scans that were not aligned to the mean_anat, and they are not on the same grid. For whatever reason i assumed that they would be because the same acquisition was used for the pre and post scan. Does the
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Dxc536
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AFNI Message Board
Hello,
I have a dataset where reviewers recommended that we analyze the pre- scan and post- scan together. In short, we are using fMRI to see our resting state data.
As a result, the plan is to align each epi to the mean T1 and then proceed with analysis. Further, I have been using slomoco instead of 3dvolreg, and the developers recommend the two not be run together.
My pipeline is as fo
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Dxc536
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AFNI Message Board
Hello,
I have data from a 2x2 repeated measures design (Time: Pre, Post, Condition: A, B) and I performed a group level analysis using 3dANOVA3 -type 4 -alevels 2 -blevels 2.
My question is how do I best display which regions showed a significant difference with respects to group and time and in what direction? Is it appropriate to create a mask based on the time_cond_interact map and the
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Dxc536
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AFNI Message Board
Hello,
I have two fMRI runs that I'm analyzing using afni proc. I've noticed in some instances the EPI's of the two runs are not aligned with eachother. Also, I have been using Align Anat2Epi, which means the two EPI's remain in non-warped form.
What's odd to me, is that after looking the stats, the results don't look all that bad (i.e. the activation is where
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Dxc536
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AFNI Message Board
Hello,
I've been outputting the 3dclusterize results using '>' in order bring them to a text file. I was wondering if there is a way to output only the cluster numbers and not all of the extra text or format the text file differently? We are performing individual subject ROI analysis across multiple different regions which means we have many text files corresponding to a vari
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Dxc536
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AFNI Message Board
I'm so sorry. You're right, it was a mistake in the argument following '1Dmatrix_apply"
Thanks for your help. I'll be more careful next time.
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Dxc536
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AFNI Message Board
3dAllineate -source Q08.DLPFC.T1.Pre+orig -master Q08.DLPFC.T1.Pre_al_keep+orig -final wsinc5 -1Dmatrix_apply Q08.DLPFC.T1.Pre+orig_al_keep_mat.aff12.1D -prefix anat_w_skull_warped
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Dxc536
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AFNI Message Board
Hello,
Here is the output for afni -ver:
Precompiled binary linux_ubuntu_16_64: Mar 20 2019 (Version AFNI_19.0.26 'Tiberius')
In order to generate the .1d file, the following command was used:
align_epi_anat.py -anat2epi -anat Q08.DLPFC.T1.Pre+orig -suffix _al_keep -epi Q08.DLPFC.RestingState1.Pre+orig -epi_base 0 -epi_strip 3dAutomask -volreg off -tshift off
Thanks,
by
Dxc536
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AFNI Message Board
Hello,
I've been trying to us 3dAllineate and the following error occurs:
** ERROR: mri_read_ascii: couldn't open file Q08.DLPFC.T1.Pre+orig_al_keep_mat.aff12.1D
This isn't the first time I've seen an error associated with mri_read_ascii. I've also seen it when I've used SLOMOCO when it was trying to read a text file containing SLOMOCO_SLICE_TIMING
does a
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Dxc536
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AFNI Message Board
Thank you! That works great!
I have two additional questions (and hopefully my last questions - thanks again for all of your help):
1) When I run 2 sessions at a time, I do get similar beta coefficients, but I get a slightly bigger T-Stat than if I run each run individually. Do you know why that is?
2) For one of my datasets, I ran the same scan twice and participants did the exact same
by
Dxc536
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AFNI Message Board
Thanks,
I'm not sure if I'm doing that correctly. When I input the two runs separately and provide two separate stim files using uber_subject.py I have to modify the second stim file times as if the two datasets are concatenated. Because of this, I am getting very different results than if I run the two files separately. Can you point me to an example afni_proc.py that uses the two
by
Dxc536
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AFNI Message Board
Hello,
I have two scenarios that I'm working with:
1) Within the same day, subjects had two different scans - one scan was moving their lefthand and one hand was moving their righthand.
for this scenario I would like a Left-Right contrast; however, I'm not sure how to do this when I'm analyzing the two separately. Using afni_proc.py I do see that I can enter multiple '
by
Dxc536
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AFNI Message Board
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