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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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Hi Rick,
Even It was installed, I still could not run AFNI, neither could I use the system check command.
Naveed
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Naveed
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AFNI Message Board
Hi Rick,
I was able to install using this command
rt5212m-paed:~ naveed qureshi$ tcsh @update.afni.binaries -bindir ABIN -no_recur -defaults -package macos_10.12_local
However R installation in not working now.
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Naveed
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AFNI Message Board
Hi Rick,
Following is the output.
rt5212m-paed:~ naveed qureshi$ curl -O
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 45323 100 45323 0 0 283k 0 --:--:-- --:--:-- --:--:-- 281k
rt5212m-paed:~ naveed qureshi$ tcsh @update.afni.binaries -defaults -package
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Naveed
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AFNI Message Board
This is a new Mac on OS 10.15 and it never had any AFNI installed.
yes update command also failed.
I tried both the app and the instruction, but both failed unfortunately.
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Naveed
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AFNI Message Board
I tried a clean install and its failed.
output from echo $0 = -bash
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Naveed
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AFNI Message Board
Hi Gang,
Thank you for your help the code is running fine now.
Yes, I forget about the centering, I will insert the flag. however, is this model correct for correcting the effects of the covariates or I need to use another tool to do the GLM?
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Naveed
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AFNI Message Board
Hi Rick,
I found this information in the acquisition files
ECG Freq Per: 0 0^M
PULS Freq Per: 58 1033^M
RESP Freq Per: 14 4100^M
EXT Freq Per: 0 0^M
EXT2 Freq Per: 0 0^M
ECG Min Max Avg StdDiff: 202 815 533 166^M
PULS Min Max Avg StdDiff: 887 2211 1024 9^M
RESP Min Max Avg StdDiff: 3020 10220 4689 1023^M
EXT Min Max Avg StdDiff: 680 30005 680 241^M
EXT2 Min Max Avg StdDiff:
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Naveed
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AFNI Message Board
Hi, Rick.
Yes, I have the physiological recordings in *.resp and *.plus format. I can't figure out how to use them with RetroTS.py. I asked this question earlier on the message board as well. Can you please help me to make a script for the procedures you mentioned?
Thank you.
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Naveed
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AFNI Message Board
I preprocessed the T1 anatomical with freesurfer separately. This file is the output of freesurfer which is the registration of DKT atlas to the subject native space.
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Naveed
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AFNI Message Board
Hi Peter,
Thank you for your reply.
I am not sure about CMRR but this data is acquired at MNI Montreal following exactly the same sequence as ADNI3.
Here are my afni_proc command and subsequent commands to generate the connectivity matrix.
afni_proc.py -subj_id $line -dsets /data/data05/Studies/MCSA/RAW/MRI/$line/$RSN -copy_anat /data/data05/Studies/MCSA/RAW/MRI/$line/$T1 -blocks de
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Naveed
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AFNI Message Board
Hi AFNI experts,
I have a multiband resting state fMRI acquisition with the following details.
Scanner = Seimens MAGNETOM prisma
TR = 0.681 sec
Number of slices per volume = 54
Number of Volumes = 870
Slice Thickness = 2.5mm
Series = Ascending
I tried to preprocess this data with afni_proc.py by converting dicoms using dcm2nii command. I believe there is an error in the data conver
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Naveed
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AFNI Message Board
Hi Afni Experts,
I am still waiting for your reply on my query.
Thank you.
Naveed
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Naveed
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AFNI Message Board
Hi Paul,
Thank you for your reply.
Yes, ROI mapping was based on the FreeSurfer non-linear registration to DKT atlas.
We converted DICOMs using dcm2nii command and run AFNI preprocessing with the nifti input to afni_proc.py
I ran @radial_correlate on the data and do not see a different pattern of correlations in both the acquisitions at 0.5 thresholds for the same subject data.
In addi
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Naveed
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AFNI Message Board
HI Afni experts,
I have multiband rs-fMRI data, acquired on a Seimens scanner, with TR=0.681s with 870 time points. This acquisition exactly follows the ADNI3 acquisition protocols.
Here is what I have started with for processing:
afni_proc.py -subj_id $line -dsets /data/data05/Studies/MCSA/RAW/MRI/$line/$RSN -copy_anat /data/data05/Studies/MCSA/RAW/MRI/$line/$T1 -blocks despike align
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Naveed
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AFNI Message Board
I have installed the latest version of AFNI now, but still error is same, please see below
naveed@cmfisher:/data/data05/naveed/1.Projects/7.MCSA_rs-fMRI/BS0001MC_20180315.results$ /data/data02/vfonov/AFNI/abin/FATCAT_matplot -ShinyFolder /home/naveed/R/x86_64-pc-linux-gnu-library/3.4/shiny/FATCAT_matplot_shiny /data/data05/naveed/1.Projects/7.MCSA_rs-fMRI/BS0001MC_20180315.results
[1] 419
na
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Naveed
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AFNI Message Board
naveed@cmfisher:/data/data05/naveed/1.Projects/7.MCSA_rs-fMRI$ @FATCAT_matplot_shiny -ShinyFolder /home/naveed/R/x86_64-pc-linux-gnu-library/3.4/shiny/FATCAT_matplot_shiny BS0001MC_20180315.results
[1] 20006
naveed@cmfisher:/data/data05/naveed/1.Projects/7.MCSA_rs-fMRI$ Error in shinyAppDir(x) : App dir must contain either app.R or server.R.
Calls: <Anonymous> ... as.shiny.appobj -> a
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Naveed
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AFNI Message Board
Hi Justin,
Thanks for your reply.
It doesn't work even with the folder path for .netcc files
naveed@cmfisher:/data/data05/naveed/1.Projects/7.MCSA_rs-fMRI$ @FATCAT_matplot_shiny -ShinyFolder /home/naveed/R/x86_64-pc-linux-gnu-library/3.4/shiny BS0001MC_20180315.results/netcorr_000.netcc
Error: BS0001MC_20180315.results/netcorr_000.netcc does not exist.
This file exists and I alr
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Naveed
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AFNI Message Board
Hi Raj,
Thanks for your detailed reply, however, the problem is still not solved.
Following are my system details:
AFNI version: Precompiled binary Debian-x86_64-1-gnu: May 17 2018 (Version Debian-18.0.05+git24-gb25b21054~dfsg.1-1~nd17.10+1+nd18.04+1)
OS: Ubuntu 18.04.1 LTS
AFNI installation is here: /usr/lib/afni/
I ran the following command but it can not find FATCAT_matplot command
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Naveed
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AFNI Message Board
Hi AFNI experts,
I am still waiting for the response on this question.
Thank you.
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Naveed
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AFNI Message Board
Thank you Paul.
It works perfectly now.
Another question is about the following error while running this command @afni_R_package_install -shiny -circos
"Fatal error: cannot open file '/usr/bin/shiny/misc/OmicCircos_pkg_install.R': No such file or directoryā€¯
Please let me know how to rectify it.
Naveed
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Naveed
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AFNI Message Board
Yes you are right here is the problem.
How can I fix it?
naveed@cmfisher:/data/data05/naveed/1.Projects/7.MCSA_rs-fMRI/BS0001MC_20180315.results$ 3dinfo -labeltable DKT_resample+orig
<VALUE_LABEL_DTABLE
ni_type="2*String"
ni_dimen="76" >
"6" "l_PUTA
"
"13" "l_IP
"
"36" "l_supraMG&
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Naveed
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AFNI Message Board
Hi Paul,
Thank you for your help. Can you please guide me about how can I insert the label table inside the ROI file?
What is the proper way to pass the label table argument in 3dNetCorr command?
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Naveed
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AFNI Message Board
Yes, I did they way to told me. I used the following command to make a table.
@MakeLabelTable -lab_file ../DKT.txt 1 0 -labeltable sub.niml.lt -dset DKT_resample+orig
then pass it to 3dNetCorr as
3dNetCorr -prefix netcorr -mask mask_GM_resam+orig.BRIK -ts_out -fish_z -inset errts_DKT_fs+orig -in_rois DKT_resample+orig -output_mask_nonnull -push_thru_many_zeros -ts_wb_corr -ts_wb_strlabel su
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Naveed
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AFNI Message Board
Hi Paul,
I made the label table with ROIs and the 3dNetCorr. Can you please let me know why the arrangement of labels in the output file is not correct. it should look like this for correct plotting with fat_mat_sel.py
# 75 # Number of network ROIs
# 2 # Number of netcc matrices
# WITH_ROI_LABELS
l_HC l_ENTH l_AG l_THAL l_CAUD l_PUTA l_PALL l_ACUM l_cACC l_cMFC l_CUN l_FG l_IP l_inf
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Naveed
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AFNI Message Board
Hello,
I want to insert a label table in the final connectivity matrix.
I generated the connectivity matrices and I am using the DKT parcellation files generated from freesurfer for the in_rois in 3dNetCorr script using the following command:
3dNetCorr -prefix netcorr -mask mask_GM_resam+orig.BRIK -ts_out -fish_z -inset errts_DKT_fs+orig -in_rois DKT_resample+orig -output_mask_nonnull -pu
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Naveed
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AFNI Message Board
Hi Paul,
I want to compute a connectivity matrix for all the voxels in the GM mask for the whole brain. How should I set my input INROIS file?
Thanks,
Naveed
by
Naveed
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AFNI Message Board
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Pages: 123