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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 2 of 4
Pages: 1234
Results 31 - 60 of 101
Hi Gang,
Thanks for the reply! It was coded as 1 and 2. Could you please let me know that if I need to rerun after coding it (sex) as -1 and 1?
Best,
JW
by
JW
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AFNI Message Board
Dear AFNI experts,
I used the below script to run a one-sample t-test.
3dttest++ \
-prefix results \
-covariates Covariate.txt \
-center SAME \
-mask /Volumes/GM_mask/GMmask+tlrc \
-clustsim \
-setA A \
subj1 /Volumes/subj1/Proc_results/nbm_final_r2z+tlrc \
subj2 /Volumes/subj2/Proc_results/nbm_final_r2z+tlrc \
subj3 /Volumes/subj3/Proc_results/nbm_final_r2z+tlrc \
subj4 /Volumes/
by
JW
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AFNI Message Board
Hi pt,
I used the 3dmaskave script below. It did work for another result and only this particular dataset continuously generates zero values. Thank you!
subjects="subj1 subj2 subj3 subj4"
for subject in $subjects ; do
echo $subject > ROIavgs.$subject.txt
for roi in 1; do
3dmaskave -quiet -mrange $roi $roi -mask Clust_mask_0001+tlrc /Volumes/$subject/Proc_results/r2z+tlr
by
JW
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AFNI Message Board
Dear AFNI experts,
I ran 3dMVM for resting-state data and got some brain regions that survived the statistical threshold. I then ran 3dmaskave to extract z scores from each surviving region, but for some reason, almost all subjects' z scores appear zero, although it seems there were no problems during extracting the data. I have attached the screenshot of the terminal and extracted values
by
JW
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AFNI Message Board
Dear AFNI experts,
I used the below script to run a one-sample t-test.
3dttest++ \
-prefix results \
-covariates Covariate.txt \
-center SAME \
-mask /Volumes/GM_mask/GMmask+tlrc \
-clustsim \
-setA A \
subj1 /Volumes/subj1/Proc_results/nbm_final_r2z+tlrc \
subj2 /Volumes/subj2/Proc_results/nbm_final_r2z+tlrc \
subj3 /Volumes/subj3/Proc_results/nbm_final_r2z+tlrc \
subj4 /Volumes/
by
JW
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AFNI Message Board
Hi Rick,
Thank you for checking this and for your email reminder! I did try dcm2niix_afni as suggested by Daniel and seemingly it is working. Below is the screenshot of the functional image that was processed using dcm2niix_afni.
Best,
JW
by
JW
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AFNI Message Board
Hi pt,
Thank you for your thoughts. Also, thank you for the correction. Sorry, it was a typo - I meant to say "the gap between the task can't be treated as resting-state". Have a good weekend!
Best,
JW
by
JW
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AFNI Message Board
Hi pt,
A gap between events was 3 sec. I agree that the gap between the task can be treated as resting-state. I was searching for if the between-task time-series data could be meaningful and if it is possible to investigate this using AFNI. Thank you so much for your thoughtful answer. It really helped!
Best,
JW
by
JW
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AFNI Message Board
Dear AFNI experts,
I'm looking forward to learning how to regress out the task-related time-series and to get the non-task related time-series using the task-related fMRI data. Thank you in advance for your help!
JW
by
JW
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AFNI Message Board
Dear AFNI experts,
I used the below to3d script for functional data.
to3d -epan -assume_dicom_mosaic -oblique_origin -prefix epi.resting -time:zt 64 404 1400 alt+z SerieMR-0004-*.dcm
And, had error below.
++ to3d: AFNI version=AFNI_19.3.11 (Nov 1 2019) [64-bit]
++ Authored by: RW Cox
++ It is best to use to3d via the Dimon program.
*+ WARNING: TR expressed in milliseconds will be
by
JW
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AFNI Message Board
Dear AFNI experts,
I am interested in looking at the resting-state component of the time series during task-based fMRI data. So for task-based fMRI, we are trying to find what parts of the time-series match the task design, and we are ignoring all of the residual error which in this case actually is the resting-state component of the time series. I understand how can we sort out task-related a
by
JW
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AFNI Message Board
Dear AFNI experts,
I have another issue with the alignment using the below script.
align_epi_anat.py \
-epi2anat \
-anat "$subj"."$cond"_SurfVol.nii \
-epi epi."$subj"."$cond".slicemocoxy_afni.slomoco+orig \
-epi_base 0 \
-anat_has_skull yes \
-epi_strip 3dAutomask \
-cost lpa \
-volreg off \
-overwrite
I wanted to fix the alignment in the
by
JW
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AFNI Message Board
Hi pt,
Thank you for checking this! Below is the result of the command you suggested.
0.000 "$subj"."$cond"_SurfVol.nii
0.000 epi."$subj"."$cond".slicemocoxy_afni.slomoco+orig
I rant the script without the -giant_move, but there are still misalignments (see the attached image).
Best,
JW
by
JW
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AFNI Message Board
Dear AFNI experts,
I used align_epi_anat.py to align anat and epi files before running the proc py using the below script.
align_epi_anat.py \
-epi2anat \
-anat "$subj"."$cond"_SurfVol.nii \
-epi epi."$subj"."$cond".slicemocoxy_afni.slomoco+orig \
-epi_base 0 \
-anat_has_skull yes \
-epi_strip 3dAutomask \
-giant_move \
-volreg off \
-overwr
by
JW
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AFNI Message Board
Hi Daniel,
Thank you so much for the instruction. I'll try one of those.
Best,
JW
by
JW
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AFNI Message Board
Dear AFNI experts,
I extracted some masks of my interest from the DD_Desai_MPM (TT_desai_DD_MPM+tlrc) atlas, but my functional data were normalized to the MNI152_T1_2009c. Could anyone please let me know if there is a way that I can convert the mask in the mask from the TT space to the MNI152 or do I need to rerun the proc py using TT_152_2009c as a basis? Thank you in advance for your help!
by
JW
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AFNI Message Board
Hi Gang,
Thanks again for the suggestion. So you are suggesting normalize the four errts files using 3dMean or 3dcalc before submitting to either 3dttest or 3dLME?
Best,
JW
by
JW
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AFNI Message Board
Hi Gang,
No, I don't want to compare the 4 runs. Each subject was scanned for two resting state sessions (REST 1 and REST 2) over a period of two days. During each session, data were collected using both the left-right (LR) and right-left (RL) phase-encoding runs. I want to treat the 4 runs (REST1 LR, REST1 RL, REST2 LR, REST2 RL) as 1 run. I initially tried to concatenate the 4 epi files
by
JW
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AFNI Message Board
Hi Rick,
Thank you for the clarification. Right, I meant Fischer transformed seed-based correlation volumes (that was computed from errts files). I was wondering if these 4 separate scans for each subject can be submitted to 3dttest+ or 3dLME and can be treated as one run for each subject or should I normalize them into one.
Best,
JW
by
JW
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AFNI Message Board
Hi Rick,
Thank you so much for the thoughtful comments. These really help. I'll pre-process each run separately. I only ran 3dTcat so that should be the original dimension?
Could you please clarify one more thing? After running the preprocessing separately, would it make sense to include each into the group analysis? For example in the 3dttest++, would the below be possible?
-setA
by
JW
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AFNI Message Board
Hi pt,
Thank you so much for the suggestion. Below is the 3dinfo of the concatenated epi data.
Dataset File: trunc_rest_100307+orig
Identifier Code: AFN_snRM4ak1fqyJqtzOpLs2Ag Creation Date: Mon Nov 16 21:55:36 2020
Template Space: ORIG
Dataset Type: Echo Planar (-epan)
Byte Order: LSB_FIRST
Storage Mode: BRIK
Storage Space: 12,896,133,120 (13 billion) bytes
Geomet
by
JW
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AFNI Message Board
Dear AFNI experts,
Hope you all are staying safe. I downloaded unprocessed resting-state data from the Human Connectome project where they had 4 scans for each participant (Session 1 L to R, Session 1 R to L, Session 2 L to R, Session 2 R to L). These 4 epi data were concatenated using 3dTcat and submitted to the proc py script like below.
afni_proc.py \
-blocks despike align tlrc volr
by
JW
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AFNI Message Board
Dear AFNI experts,
I want to extract a region from the MNI_caez_mpm_22 and was trying the below command which showed the error below.
hlhp-105:NBM titus$ 3dcalc -a "MNI_caez_mpm_22::Area_1" -expr a -prefix Area1
++ 3dcalc: AFNI version=AFNI_19.3.11 (Nov 1 2019) [64-bit]
++ Authored by: A cast of thousands
++ WARNING: file /Users/titus/.afni.log is now 1509520280 (1.5 billion)
by
JW
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AFNI Message Board
Dear AFNI experts,
Hope everyone is staying safe and healthy. I am trying to use the basal forebrain mask in the SPM Anatomy Toolbox mask as a seed mask for the resting state analysis in AFNI. I downloaded the mask from the SPM webpage and converted the SPM mask to the standard MNI using @ShiftVolume -MNI_Anat_to_MNI.
I tried this earlier which showed a mask in the first attached screenshot.
by
JW
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AFNI Message Board
Hi Gang,
Thank you for the instruction. I'll try that. Stay safe!
Best,
JW
by
JW
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AFNI Message Board
Hi Gang,
Thank you! Could you please let me know if you meant to remove this line?
-gltLabel 5 'Post-Pre' -gltCode 5 'Time : 1*post -1*pre' \
Also, could you please let me know if it is correct to have Group : Time F on both OLay and Thr?
Best,
JW
by
JW
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AFNI Message Board
Dear AFNI experts,
Hope all of you are staying safe. I am running 3dLME and am wondering how can I analyze Group by Time effects. I have two groups of subjects (A and B) and both groups have before (pre) and after (post) data. Below is the script I used.
3dLME -prefix 3dLME -jobs 5 \
-model 'Group*Time' -ranEff '~1' -SS_type 3 \
-num_glt 5 \
-gltLabel 1 'Apost-Ap
by
JW
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AFNI Message Board
Hi Gang,
Thanks and sorry it was a silly question. Can I have one more question about the result? I found a greater activation in right inferior frontal gyrus after running this, but am not sure how to interpret this. Could you please advise how to interpret the interaction between genotype x group x time results?
Best,
Jun
by
JW
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AFNI Message Board
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Pages: 1234