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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
Results 1 - 30 of 48
Hello experts. I am currently working with elderly population. I would like to have any suggestion related to the best indicator that I should use to control/covariate for gray matter atrophy in my analysis.
Thank you for your advices!!!
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LuisaBoh
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AFNI Message Board
Hello AFNI. I am running the following group comparison without an specific mask:
3dttest++ \
-prefix HighvsLowICG_noCov_noMask \
-prefix_clustsim HighvsLowICG_noCov_noMask \
-tempdir /scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp \
-center SAME\
-Clustsim 24 \
-toz \
-setA HighICG \
-230 r_CBF_GMC_80.nii.gz \
-....
-setB LowICG
by
LuisaBoh
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AFNI Message Board
Hi Gang, here is my script. I am trying to see the main effect of loneliness, main effect of hamd and their interaction in my CBF maps. would you mind to tell me if I am doing it correctly?
3dMVM -prefix 3dMVM_test -jobs 24 \
-mask GM2mm_WFU_Mask.nii.gz \
-bsVars 'loneliness+age+gender+hamd' \
-qVars 'age,gender' \
-num_glt 3
by
LuisaBoh
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AFNI Message Board
Hi Gang thanks for answering me, I feel very confused with the design of my 3dMVM script, would you mind to help me a bit?
I want to see the relationship between the CBF_maps (voxel wise, .nii file per subject) with a quantitative clinical measure (loneliness, which is one single number per subject). I need to control for age, gender, depression scores and gray matter concentration (the gray mat
by
LuisaBoh
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AFNI Message Board
Hi, to be more specific.
My dependent variable is CBF map (50 in total, one for each subject)
My independent variable is the clinical measure (50 in total, one number for each subject)
My covariates are: age, gender and GMC: gray matter concentration (the GMC is map which is nifti file)
by
LuisaBoh
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AFNI Message Board
Hello AFNI
I have CBF maps for 50 subjects.
I want to know if they are any significant relationships between the CBF concentration and a clinical score (one number per subject) after controlling for age, gender and gray matter concentration.
Which program do you suggest me to do this analysis?
Thank you :)
by
LuisaBoh
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AFNI Message Board
Thank you so much for your help!! last question, this result means that my Pearson r correlation value to p=0.001 is 0.495?? Im confused with the sign of the correlation because the results in the AFNI GUI is showing me negative Pearson values. According with your experience, what is the "appropriate" way to report this result? (attached is a picture of my results)
$ p2dsetstat -2si
by
LuisaBoh
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AFNI Message Board
Hello I realize that I was using the arguments of the command in a wrong order, now I change them and it woks!!!
Now I have another question, how can I threshold this results? I know that with the 3dttest++ I can use the flag clustSim to obtain the table for thersholding but I am not sure what is the best approach when using 3dTcorr1D, any suggestions?
by
LuisaBoh
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AFNI Message Board
Hello AFNI
I am trying to correlate my concatenate CBF_maps of 41 subjects with a clinical score. I am using 3dTcorr1D with the -mask flag. I am confused because it seems that the correlations are not made inside the mask I am giving to the program, what am I doing wrong? Attached is a picture of my mask (in red) and my correlation results (in blue)
Here is my command:
3dTcorr1D -prefi
by
LuisaBoh
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AFNI Message Board
Hello AFNI
I ran 3dttest++ to compare the CBF values of 2 groups. I used the -mask flag which is supposed that restrict my analysis to the mask I am using (just gray matter excluding cerebellum) and I am having results that are showing me some white matter voxels, what am I doing wrong? Here is my 3dttest code
3dttest++ -mask GMmask__MNI152_2009_noCerebellum_final.nii \
-prefix Grief
by
LuisaBoh
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AFNI Message Board
Hi. I am trying to match 2 files and I would like some help. I found they had different delt and ornt so I resample them and still not matching, any suggestions?
3dinfo -header_line -prefix -same_all_grid ASL_CBF_2MNI_6mm_172_120916.nii GCmask_MNI152_2009_noCerebellum.nii
prefix =dim? =delt? =ornt? =cent
by
LuisaBoh
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AFNI Message Board
Hi Gang!!! I did what you suggest but I am having the following error: ERROR: -permute failure for unexplainable reasons /:(
Also, would you mind to suggest me how to interpret these results assuming the 3dtest++ is running without errors?
(base) lbohorquez@PSYC-CRI-10822:~/Desktop/RCC_no$ ./3dttest_ANGER_regression.sh
++ 3dttest++: AFNI version=AFNI_20.1.06 (May 4 2020) [64-bit]
++ Auth
by
LuisaBoh
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AFNI Message Board
Probably I didn't explain correctly. My grief_score is the score of one of my clinical test, just a number. I want to know if this score can be predicted or have any correlation with the activation maps of my fMRI task, including the gray matter concentration (per voxel), age and gender as covariates.
If I include my faces_gr_shapes_avg.nii as a covariate in the 3dttest++, what can I use
by
LuisaBoh
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AFNI Message Board
Hello Gang yes!
grief_score ~ brain_ activation (per voxel) + age + gender + gray_matter_ concentration (per voxel)
by
LuisaBoh
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AFNI Message Board
Hi AFNI
I was wondering if you can suggest me which of your programs could help me to identify clinical correlations between fMRI data and clinical scores but having as covariates age, gender and voxel wise map of gray matter concentration for each subject.
In other words I want to know if one of my clinical scores (grief_score) can be predicted by the fMRI activations of my task. Considering
by
LuisaBoh
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AFNI Message Board
Daniel thank you so much for your help!
Yes I have pre-steady data, when you say "use that as an external volreg_base_dset" you are referring to change the epi_base to 1? (sorry if this is a dumb question)
# ================================= align ==================================
# for e2a: compute anat alignment transformation to EPI registration base
# (new anat will be curr
by
LuisaBoh
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AFNI Message Board
Daniel thank you so much! it improves A LOT but still not my favorite what do you think?
Here is what I used
-align_opts_aea -cost lpa+ZZ -big_move -check_flip
by
LuisaBoh
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AFNI Message Board
Hi AFNI!
I am running afni_proc but I am having an issue aligning my EPI to my T1. My datasets are very close that's why I change the option -giant_move for big move and the results are better but still not good. I also tried with LPC+ZZ and is not different than the picture attached. Any suggestions? Here is my command
afni_proc.py \
by
LuisaBoh
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AFNI Message Board
Hello AFNI friends
I am very confused with a result that I had from 3dttest++. According to the CSimA.NN3_bisided.1D table, I set the voxel the in the GUI to 0.05, the minimal cluster size should be >22925 voxels to be significant , which corresponds to p < 0.05 corrected, so I click in clusterize change the NN3 and set the cluster size to 22925 and nothing survived ...BUT if I change
by
LuisaBoh
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AFNI Message Board
Thank you so much Daniel, that was super helpful!
Have a nice day :)
by
LuisaBoh
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AFNI Message Board
Hello AFNI
I want to extract the cerebellum of the subrick 4 "GC_mask" of the MNI152_2009_template_SSW.nii. Would you mind to guide me how to do it?
Thank you
by
LuisaBoh
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AFNI Message Board
Hi AFNI
I was wondering if someone can give me an advice. For an fMRI preprocessing, what is more recommended, 3dTshift before or after field map correction?
Do you have any reference to read?
by
LuisaBoh
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AFNI Message Board
3dinfo -slice_timing EPI_retroicor.nii
0.000000|1.000000|0.055556|1.055556|0.111111|1.111111|0.166667|1.166667|0.222222|1.222223|0.277778|1.277778|0.333333|1.333334|0.388889|1.388889|0.444444|1.444445|0.500000|1.500000|0.555556|1.555556|0.611111|1.611112|0.666667|1.666667|0.722222|1.722223|0.777778|1.777778|0.833333|1.833334|0.888889|1.888890|0.944445|1.944445
3dinfo -slice_timing EPI_tshift.
by
LuisaBoh
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AFNI Message Board
Hello AFNI experts!!
I am having an issue with my fMRI data. I found that when I do 3dinfo -slice_timing in my EPI images the timing is "0". We found a solution to "called back" the slice timing information 3dTcat topup_corrected_Rest.nii -tpattern alt+z -prefix EPI_fixed.nii which seems to work. But when I want to use this “fixed” data, and do, for example 3dTshift, the s
by
LuisaBoh
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AFNI Message Board
Hello I am trying to install the programs necessary to open uber_subject.py but its been almost impossible. Would you mind to give me any advices please?
Here is my afni_system_check.py output
Thank you
------------------------------ OS specific -------------------------------
XQuartz version : 2.7.11
which brew : /usr/local/bin/brew
brew version : Homebrew 2
by
LuisaBoh
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AFNI Message Board
Hello AFNI experts
I am working in an emotional fMRI task. I am interested to see the activations in different contrasts: faces vs shapes, anger vs neutral, fear vs neutral, fear+anger vs neutral.
I have the stats for the faces vs shapes, anger vs neutral, fear vs neutral, which are activation maps generated running 3dDeconvolve (the bucket output).
I made 3dcalc -a file’[39]’ -expr “a*
by
LuisaBoh
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AFNI Message Board
it didn't work but I can make it work if I type
export DYLD_LIBRARY_PATH=/opt/X11/lib/flat_namespace
afni
I guess I will always do it in this way haha
Thank you Rick for your time
by
LuisaBoh
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AFNI Message Board
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