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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
Page 3 of 4
Pages: 1234
Results 61 - 90 of 101
Dear AFNI experts,
I was trying to run 3dMVM for 2 between subject variables (genotype and group) and 1 within subject variable (Time) with the below 3dMVM command based on AFNI 3dMVM instruction example 2, but kept getting the error message saying 'Failed at GLT No. 1! Make sure that the model or GLT specification syntax is correct'. Could you please let me know what would be the pr
by
JW
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AFNI Message Board
Hi Daniel,
Thanks for the clarification! That really helps.
Best,
Jun
by
JW
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AFNI Message Board
Hi Daniel,
Thank you so much for the instruction. Could you please clarify one thing? I am a little bit confused by the last step (resample to EPI grid (grid of some dataset in MNI space) starting with the atlas again) for the two reasons.
First, I could not find epi_r1_MNI+tlrc in the directory you suggested. I could only find epi_r1+orig. Did I make a mistake when installing AFNI or can
by
JW
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AFNI Message Board
Dear AFNI experts,
I am interested in extracting cerebellum segmentation mask from SUIT cerebellum probabilistic mask (attached) and use that segmentation for the seed for resting-state analysis. Could you please let me know if there is any way to extract the each component mask?
Best,
JW
by
JW
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AFNI Message Board
Hi pt and Daniel,
Thank you so much for your help. I'll try both ways. Really appreciate it!
Best,
by
JW
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AFNI Message Board
Hi pt,
Thanks again for the explanation. That makes sense to me. I have tried the command you suggested and the anterior command works well but the posterior command comes with the following warning message (*+ WARNING: output sub-brick 0 is all zeros!). I also tried 3dcalc -a DSET -expr 'a*(isnegative(y-5))' -prefix DSET_POST but it also showed the same warning message. Could you pl
by
JW
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AFNI Message Board
Hi pt,
Thank you so much. It works very well. Could you also advise me how to create anterior and posterior hippocampus mask?
Best,
by
JW
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AFNI Message Board
Dear AFNI experts,
I am working on creating hippocampal mask as a seed region for resting state analysis and am trying to use follow_ROI_aaseg+tlrc that was created after created after proc py 11 with freesurfer. Below is the command I am trying to use to extract create masks of left and right hippocampi extracted from follower aseg dataset (normalized in preprocessing script). I am not sure i
by
JW
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AFNI Message Board
Dear AFNI experts,
Below is the script we used to preprocess my EPI (task-based) data. We are looking for pre-processed but non-statistically analyzed data so we removed regress options.
afni_proc.py \
-anat_has_skull yes \
-blocks despike tshift align tlrc volreg mask scale regress \
-copy_anat mprage/mprage.${subj}.${cond}+orig \
-dsets /Users/lab/Desktop/AES2016_FNT/$
by
JW
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AFNI Message Board
Dear AFNI experts,
Could you please let me know how can I find pre-processed but non-statistically analyzed data from proc.py output?
Below is the script I used.
afni_proc.py \
-anat_has_skull yes \
-blocks despike tshift align tlrc volreg mask scale regress \
-copy_anat mprage/mprage.${subj}.${cond}+orig \
-dsets /${subj}/${subj}.${cond}/${subj}.${cond}+orig \
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by
JW
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AFNI Message Board
Dear AFNI experts,
I had a below error while running to3d.
titus% to3d -anat -assume_dicom_mosaic -oblique_origin -prefix prefix image*.dcm
++ to3d: AFNI version=AFNI_19.1.09 (May 17 2019) [64-bit]
++ Authored by: RW Cox
++ It is best to use to3d via the Dimon program.
++ WARNING: file /Users/titus/.afni.log is now 570375242 (570 million) bytes long!
++ Counting images: total=208 2
by
JW
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AFNI Message Board
Dear AFNI experts,
Could you please let me know what would the motion regressors and other noise regressors output files look like after completing proc py?
Best,
Jun
by
JW
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AFNI Message Board
Dear AFNI experts,
Could you please suggest any strategies to enhance SNR in already collected resting state data? I am working on suggesting an alternative strategy for a study proposal and am wondering what can I suggest for a possible alternative strategy.
Best,
Jun
by
JW
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AFNI Message Board
Hi Rick,
Thank you for the explanations and suggestion. This really helps in understanding the correct and incorrect trials. I'll check with the posting you suggested.
Can I have one more question that is seemingly a little bit off from this but still related issue. I am checking with number of TRs for each stim files and @ss_reivew_basic says num TRs per stim (orig) : 190 199 202.
by
JW
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AFNI Message Board
Hi Rick,
Thanks for the response. This is really helpful. Could you please clarify one more thing? You mentioned that 'by not including them in the model, such times are consider to be baseline'. Does this mean they were completely removed and censored from the model? If so, could you also please let me know how can I check these in the afni proc.py output folder?
Thanks,
Jun
by
JW
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AFNI Message Board
Dear AFNI experts,
We ran an AFNI proc.py for task-based analysis and excluded incorrect trials from stim files. As far as we understand, 3dDeconvolve does not model the incorrect trials because we did not include in the stim files. However, the TRs for the incorrect trials still included in the analysis. Could you please clarify if we are understanding correctly?
Best,
Jun
by
JW
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AFNI Message Board
Dear AFNI experts,
I had the below error while running resting state proc py (example 11 using Freesurfer).
3dTproject -polort 3 -prefix rm.det_pcin_r01 -censor rm.censor.r01.1D -cenmode KILL -input pb02.subj.time1.r01.volreg+tlrc
++ 3dTproject: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: Cox the Algebraic (Linear)
++ input time points = 176 ; censored = 176 ; remain
by
JW
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AFNI Message Board
Hi Rick,
Thanks again for your help. Just faced an another issue when running resting state proc py for other participant's data. It showed the message below and stopped running.
*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0
echo -- GCOR = `cat out.gcor.1D`
cat out.gcor.1D
-- GCOR = 0.0541623
3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr a*b -prefix rm.DP
by
JW
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AFNI Message Board
Hi Rick,
Thanks for the reply. Yes, I have run @Align_Centers for both EPI and anat (@Align_Centers -base MNI152_T1_2009c+tlrc -dset anat+orig). It created EPI.shift.1D and anat.shift.1D. Can I rerun proc using these files?
Thanks,
Jun
by
JW
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AFNI Message Board
Hi Rick,
Thank you so much for the reply. Just have a quick question regarding your suggestion. I am not sure how to use @Align_Centers.
AFNI instruction says it should be @Align_Centers <-base BASE> <-dset DSET>. I am confused how to place anat and epi data using this script. Could you please advise?
Have a good weekend,
Jun
by
JW
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AFNI Message Board
Hi Rick,
Thank you so much for the response. Below is the output.
titus% 3dinfo -prefix -n4 -orient -o3 follow_ROI_FSvent+tlrc rm.det_pcin_rall+tlrc
follow_ROI_FSvent 96 114 96 1 LPI 95.000000 131.000000 -77.000000
rm.det_pcin_rall 96 114 96 237 LPI 95.000000 131.000000 -77.000000
Have a good rest of the weekend,
Jun
by
JW
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AFNI Message Board
Dear AFNI experts,
I encountered the following error during resting state analysis (example 11) when their proc scripts reached 3dpc. The error message is completely new to me so I don't know what needs to be fixed.
3dpc -mask follow_ROI_FSvent+tlrc -pcsave 3 -prefix rm.ROIPC.FSvent rm.det_pcin_rall+tlrc
++ 3dpc: AFNI version=AFNI_17.1.10 (Jun 6 2017) [64-bit]
** ERROR: covariance d
by
JW
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AFNI Message Board
Hi dowdlelt,
Thank you so much for your help! I'll take a look at the link you sent as well as @SSwarper.
Best,
Jun
by
JW
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AFNI Message Board
HI dowdlelt,
Thank you so much for your comment! I'll try without the line. Could you please let me know what is the difference between adding that line and without the line?
Thanks,
Jun
by
JW
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AFNI Message Board
Hi AFNI experts,
#!/bin/tcsh
foreach subj (`ls -d /Volumes/JW/AES2016/data/AES* | sed 's/\// /g' | awk '{print $5}'`)
foreach cond (Ex Rest)
echo "subj = " ${subj} ", cond = " ${cond}
cd /Volumes/JW/AES2016/data/AES101/${subj}.${cond}
afni_proc.py
by
JW
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AFNI Message Board
Dear AFNI experts,
I have a question regarding 3dttest++.
I have run a 3dttest++ with the below script.
3dttest++ -paired \
-clustsim -prefix 3dttest++_Ex-Rest \
-mask sub26/sub26.Condition2/results/mask_group+tlrc \
sub101 'stats.sub101.Condition1+tlrc.BRIK[10]' \
sub102 'stats.sub102.Condition1+tlrc.BRIK[10]' \
sub104 'stats.sub104.Condition1+tlrc.BRIK[10]
by
JW
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AFNI Message Board
Good afternoon AFNI experts,
I am trying to make activation map using 3dmerge with pthrshold and clustsize from 3dClustsim based on 3dLME map that I already have got. The 3dclustsim result looks like the below.
# 3dClustSim -mask /Volumes/BRAINSMITH_DS/Titus/AES2016_FNT/Scripts/3dLME_Ex_Rest/3dLME_021218+tlrc -acf 0.687615103 4.503241034 16.34768621 -nodec -prefix 3dClustSim
# 2-sided thre
by
JW
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AFNI Message Board
Good morning Rick and PT,
Thank you so much for the quick response. I reanalyzed based on your comments and it is now working well. I really appreciate your help!
Best,
Jun
by
JW
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AFNI Message Board
Hi AFNI experts,
I have a question regarding resting state proc.py. The below is the script I used for the analysis and its from output -help afni proc.py.
afni_proc.py -subj_id subj123 \
-dsets epi_run1+orig.HEAD \
-copy_anat anat+orig \
-blocks despike tshift align tlrc volreg blur mask regress \
-tcat_r
by
JW
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AFNI Message Board
Page 3 of 4
Pages: 1234