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 4
Pages: 1234
Results 1 - 30 of 101
Thanks Gang! The problem was resolved using the link you provided.
Best,
JW
by
JW
-
AFNI Message Board
Hi Gang,
The script worked well, but it showed another error when I was trying to run a similar one today, with the error message below.
$ ./3dMVM_script
Fatal error: cannot create 'R_TempDir'
Could you please advise how to address this issue?
Best,
JW
by
JW
-
AFNI Message Board
Hi Gang,
The script works well after the update. Thank you!
Best,
JW
by
JW
-
AFNI Message Board
Dear AFNI experts,
I am running 3dMVM and the script was working fine, but when I tested it again recently, it is not working with the error message below.
Reading input files now...
Reading input files: Done!
Range of input data: [0.000, 192.006]
If the program hangs here for more than, for example, half an hour,
kill the process because the model specification or the GLT coding
by
JW
-
AFNI Message Board
Dear AFNI experts,
I have used other neuroimaging software package to preprocess ASL data and would like to use AFNI's 3dMVM for the group analysis. My question is that how can I create the mask for the group analysis. I have MNI space registered absolute CBF map and FreeSurfer processed T1 images for each participant. I would like to create the whole brain map (i.e., not just focusing on
by
JW
-
AFNI Message Board
Hi pt,
Thank you so much for the help! align epi anat was performed prior to the proc py. volreg was removed since using epi_al+tlrc generated an error message that volre should be removed in the proc py script.
I realized that SUMA on the freesurfer outputs wasn't administered so performed SUMA and the alignment looks good. Thanks!
Best,
JW
by
JW
-
AFNI Message Board
Dear AFNI experts,
I ran align_epi_anat.py below which generated align_tlrc.jpg attached. For this, both anat (T1) and epi files were generated as tlrc format.
align_epi_anat.py \
-epi2anat \
-anat T1w_acpc_dc_restore.nii.gz \
-epi ${subj}_REST1_LR+orig\
-epi_base 0 \
-volreg off \
-cost lpa+ZZ \
-big_move \
by
JW
-
AFNI Message Board
Dear AFNI experts,
I faced this error message while running the proc py example 11 resting state analysis. Could you please let me know what is the problem and how to address this?
Best,
JW
** ERROR: covariance diagonal (1,1) = 0
** ERROR: covariance diagonal (2,2) = 0
** ERROR: covariance diagonal (3,3) = 0
** ERROR: covariance diagonal (4,4) = 0
** ERROR: covariance diagonal (5,5)
by
JW
-
AFNI Message Board
Dear AFNI experts,
I am preparing to analyze human connectome project DTI data and there are four different scans for each participant (scan_1_AP, scan_1_PA, scan_2_AP, and scan_2_PA). Scan 1 and 2 have different bvec and bval (please see below). For this case, could you please advise how to proceed the preprocessing? Should it be scan 1 and 2 separately or both scans should be concatenated fr
by
JW
-
AFNI Message Board
Hi Justin,
Thank you so much!
I tried Rscript -e "install.packages(c('afex'),repos='; first prior to installing cmake, which failed. But, after installing cmake and running the Rscript, 3dMVM works. It still shows in afni_system_check that missing R packages though. I really appreciate your help!
Best,
JW
by
JW
-
AFNI Message Board
Hi Rick,
Thank you for the update. Please keep me posted.
Best,
JW
by
JW
-
AFNI Message Board
Hi Gang,
Thank you for the suggestion. Right, I need to use 3dMVM. I installed afex in R as you suggested and ran 3dMVM, but showed the below error message.
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
Error in library("afex") : there is no package called ‘afex’
I am not sure why it can
by
JW
-
AFNI Message Board
Thank you Rick! Even after installing gfortran, it shows the below message.
checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE
oo Warning:
These packages are not installed on the computer: afex!
These packages are not installed on the computer: brms!
These packages are not installed on the computer: metafor!
I didn
by
JW
-
AFNI Message Board
Dear AFNI experts,
I am having an issue installing R packages and below is the output of sudo rPkgsInstall -pkgs ALL.
updating R_LD_LIBRARY_PATH ...
Warning: dependencies ‘jtools’, ‘cmdstanr’ are not available
also installing the dependencies ‘RcppEigen’, ‘quantreg’, ‘TMB’, ‘RcppArmadillo’, ‘sf’, ‘units’, ‘lme4’, ‘car’, ‘nloptr’, ‘glmmTMB’, ‘rstanarm’, ‘rstan’, ‘shinystan’, ‘projpred’, ‘s
by
JW
-
AFNI Message Board
Dear AFNI experts,
I just ran proc.py (example 11 with FreeSurfer) for the resting state fMRI data. I was then checking the data quality and found that nothing was shown when errts.fanaticor file was overlayed to anat.final file for this participant (the first image attached). I did align the epi and anat files using the align_epi_ant command (the second image attached), so I am not sure what
by
JW
-
AFNI Message Board
Dear AFNI experts,
I faced the below error message while running resting-state proc py (example 11).
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./vr_base_min_outlier+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the
by
JW
-
AFNI Message Board
Hi Gang,
Sorry for the confusion. So I used coordinates from Power et al. 2011 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3222858/) to create nodes for the default mode network, salience network, and frontoparietal network based on resting-state functional data which were collected for both pre- and post-intervention. The default mode network has 59 ROIs, salience network 18 ROIs, and front
by
JW
-
AFNI Message Board
Hi Gang,
Thank you for the suggestion. I took a look at both the RBA and MBA pages including your youtube instruction (https://www.youtube.com/watch?v=K2nW8M3sYNY), which were very helpful.
Could I ask follow-up questions?
1) I am interested in performing within and between network analysis so I assume I need to use MBA?
2) More specifically, I have several ROIs from each network. On the
by
JW
-
AFNI Message Board
Dear AFNI experts,
I got outputs from 3dNetCorr and would like to do group analyses. To my best understanding, fat_mvm_prep.py and fat_mvm_scripter.py should be used to perform group analysis. Could you please let me know if I understand correctly or if there is any other option to conduct group analyses for the 3dNetCorr outputs?
Best,
JW
by
JW
-
AFNI Message Board
Hi pt,
It works well! Thank you so much! Sorry for the continuous questions but could I add one more question on this thread?
I would like to compute within- (average of all edges (nij) within the network) and between-network (average of all edges between nodes of the networks) connectivity. Could you please let me know if it is possible to directly compute these using 3dNetCorr?
Best,
by
JW
-
AFNI Message Board
Hi pt,
Thank you! I'll wait for the outputting zeros options. Keep me posted!
Have a good weekend,
JW
by
JW
-
AFNI Message Board
Hi pt,
Thank you so much for the thoughtful comments. I'll be really careful about this and will talk to my advisor about this too.
Could I have one more question that is related to 3dNetCorr? In the 3dNetCorr output, I think the command naturally sorts out the 0 values. I am wondering if there is any way I can include 0 values into the output so that I can easily gather information o
by
JW
-
AFNI Message Board
Hi pt,
Thank you again! I used the example 11 resting-state analysis of proc py which has the FreeSurfer option. Anat_final file (MNI warped) should be used for each errts files mask so the two runs don't share the exact same mask. Do you think I need to rerun the proc.py?
I also googled about the approach using the Power atlas and it seems reasonable to exclude some ROIs (especially s
by
JW
-
AFNI Message Board
Hi pt,
Thank you for the suggestion. After editing the text file according to your suggestion, a matrix with r values and z scores was generated.
There is one thing that still makes me confused though. In my analysis, there are two time points for each subject. I just ran 3dNetCorr for a single subject and in the .netcc output, there were 232 ROIs for time 1 and 249 ROIs for time 2, even th
by
JW
-
AFNI Message Board
Hi pt,
Thank you (always) for your help and quick response.
Yes, the txt file has 3 columns (x-, y- and z-coord values). Could you clarify what should be the 'ROI value' in the 4th column? I attached a screenshot of Power et al. (2011)'s coordinate excel file. The 4th column should be the Master Assignment column that divides the coordinates into each network (e.g., DMN, DAN
by
JW
-
AFNI Message Board
Dear AFNI experts,
I am interested in analyzing the correlation matrix between nodes using Power et al. (2011). There are 264 regions of interest in the Power atlas.
Power, J. D., Cohen, A. L., Nelson, S. M., Wig, G. S., Barnes, K. A., Church, J.
A., . . . Petersen, S. E. (2011). Functional network organization of the
human brain. Neuron, 72(4), 665-678. doi:10.1016/j.neuron.2011.09.006
by
JW
-
AFNI Message Board
Hi pt,
Thank you for the advice. I found that FreeSurfer output was not in diffusion space. After mapping the FreeSurfer output in the diffusion space, it worked well.
Best,
JW
by
JW
-
AFNI Message Board
Dear AFNI experts,
I created the left hippocampal mask from FreeSurfer segementation and tried to extract FA values using 3dmaskave, which showed the below error.
++ WARNING: file /Users/titus/.afni.log is now 7359264127 (7.4 billion) bytes long!
++ 3dmaskave: AFNI version=AFNI_19.3.11 (Nov 1 2019) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
by
JW
-
AFNI Message Board
Page 1 of 4
Pages: 1234