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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 31 - 58 of 58
Hello afni experts,
I would like to know how I can enter regressors that I created outside of afni into afni_proc.py for nuisance regression in a resting state analysis. I ca not find the answer. Is there a specific format that the files should have? Does .txt work?
I have a .txt file that contains 10 columns separated by tabs (compcor regressors (5 principal components for wm, 5 PC for cs
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carolin31
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AFNI Message Board
hello afni experts,
I would like to run a resting state analysis and include a file that contains compcor regressors (5 principal components for wm, 5 PC for csf) for nuisance regression which I created using a different software. After reading through afni_proc.py help and other documentation, it is still not clear to me what option I should use to input this file? Is it
-regress_use_stim_f
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carolin31
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AFNI Message Board
Hello afni experts,
I am doing my data processing mostly in afni (resting state), but I would like to use antsR to calculate CompCor principal component regressors for wm and csf and use them again later in afni as nuisance regressors. The input data required for the calculation of Compcor regressors should be slice time corrected, motion corrected and linear trends should be removed. So my q
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carolin31
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AFNI Message Board
Hello Afni experts,
I have a quick question here:
Do you recommend to erode fs_ap_wm.nii.gz and fs_ap_latvent.nii.gz before using it as masks for tissue based regression? Freesurfer does not do a perfect job with outlining the white matter and I want to make sure I have no GM voxels inside these masks.
(I constructed those masks usingsuma_make_spec_FS and would like to run aCompCor to derive
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carolin31
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AFNI Message Board
Dear afni experts,
I used afni_proc.py to run some preprocessing on my data and I also ran Freesurfer. I would like to generate a wm and ventricle mask using the freesurfer segmentation to then export it to CONN toolbox to run aCompCor. And then going back to afni for nuisance regression. I looked into @Suma_make_Spec_FS and I am wondering if it is possible to use this program only to generate
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carolin31
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AFNI Message Board
That makes sense and it worked! I have what I needed!
Thank you very much Paul and Rick!
Best
Carolin
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carolin31
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AFNI Message Board
Dear AFNI experts,
Because I want to use wavelet despiking on my resting state data set I ran for now only some preprocessing blocks on my data to get an idea about how bad the motion is. I have the xxx.enorm.1D and the outcount.xxx.1D files as output.
What I am trying to do now is to calculate for each subject 1) how many TRs would be censored based on the enorm if I apply a certain threshol
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carolin31
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AFNI Message Board
HI rick,
thank you so much for your quick response!
So you are suggesting to first use ants to register the anatomical image to the min outlier, and then running afni_proc.py with this registered anatomical image as anatomical dataset ?
Is there a short way to get the min_outlier without me having to run afni_proc.py twice? (one time to get the min_outlier and another time to run the anal
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carolin31
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AFNI Message Board
Dear afni experts,
Can I run afni_proc.py without the align block?
I would like to run afni_proc.py without the align block and do the alignment between the structural and functional image with ANTS afterwards as it seems to give me a better result.
However, I noticed that even with no align block, the anatomical image is used during the mask block for the WM, CSF segmentation, which is l
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carolin31
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AFNI Message Board
Hello afni experts,
I was running the @ss_review_driver script for quality control and I have a question in regard to how to read the sum_ideal.1D plot?
From the proc.py website I got the description that it shows the sum of all non-baseline regressors. I still don t really understand how to interpret those graphs and consequently how to detect mistakes in the stimulus timing.
I attached a
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carolin31
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AFNI Message Board
Hello Gang,
yes, the cluster is in one of the regions where I would expect some activation based on the literature.
I also performed an analysis using GAM instead of TENT and the analysis using GAM shows a significant cluster at this location as well.
I checked the HDR in a bigger set of voxels in this cluster. Only some look a little more reasonable (see attachment).
Caroline
by
carolin31
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AFNI Message Board
Hello Gang,
after switching my testing strategy to [] and comparing the F-statistic between TENT and TENTzero, it was obvious that TENTzero is the better choice. TENT seemed to pick up some motion (as seen by significant voxels around the edge of the brain and ventricles).
The estimated HRF's look reasonable for most voxel clusters, but I do have some that look weird (see attachment).
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carolin31
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AFNI Message Board
Thank you very much for the quick response!
I choose to capture interpretable BOLD signal and I do not expect my subjects to have anticipations for the different task conditions.
I also took a closer look at the beginning and the end tails of the BOLD curves and unfortunately the result of this inspection is inconclusive (see attached images).
Commend for attachment: The significant cluste
by
carolin31
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AFNI Message Board
Dear afni experts,
I am working on a task based fMRI analysis (still stuck at single subject level), where I am using GAM function to model regressors I am not interested in, and TENTzero to model regressors of interest (this is because I had previously a collinearity problem when using TENT for all regressors).
In order to get a better understanding, I ran two separate analysis, in one I u
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carolin31
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AFNI Message Board
Hello Gang,
I have a follow up question regarding the F-stats when using TENT. I can not find the answer in the afni slides. Maybe a stupid question.
I have a condition Lure_Object_FA, which I model in 3dDeconvolve by using 5 TENT regressors. I also performed a linear test
-gltsym 'SYM: +Lure_Obj_FA[1..3]' -glt_label 1 'Lure_Obj_FA'
What is the difference between th
by
carolin31
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AFNI Message Board
Hello Gang,
thank you very much for your quick response.
I just noticed something! The screenshot is showing how the bucket dataset looks like after REML. If I check the dataset after 3dDeconvolve, it looks different (see attachment). There is a GLT included in all regressor names in the right column.
I am not sure why this is not displayed in the dataset after REML.
And yes, the datas
by
carolin31
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AFNI Message Board
Dear afni experts,
I am using multiple basis functions for my task based fMRI analysis. GAM for the regressors I don t care about, and TENTzero (0,15,7) for the regressors I do care about. When using only TENT for all regressors, I had previously some collinearity issues in the design matrix.
I am confused about the TENTzero results:
I get one Fstat and 5 Coef and a Tstat (#0 - #4) for ea
by
carolin31
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AFNI Message Board
Dear afni experts,
I am running for the first time a task based fMRI analysis with afni. It is a very fast event related design (short events and short inter trial intervals).
I was visiting the afni bootcamp a few weeks ago and I was recommended to run my analysis with TENT function (TENT for the regressors I care about and GAM for the regressors I don t care about, as I had some collineari
by
carolin31
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AFNI Message Board
Hi,
i am using afni version=AFNI_18.1.26 and while running my script, I get the following Warning after 3dToutcount:
Warning: 2 failures of cl1_solve
What does this Warning mean? Is this a problem for my analysis and do I have to check on something?
Thanks a lot in advance for any help!
Carolin
by
carolin31
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AFNI Message Board
Hi,
I tried to use @AddEdge on one EPI data set (the min_outlier volume) and two anatomical data sets. I still have the same problem that the displayed overlap image has only light blue and dark red color (the purple color is missing) and that AddEdge seems to overlap the wrong images.
I used: @AddEdge final_epi_vr_base_min_outlier+orig. anat_final.103+orig. anat_final_2.103+orig.
after
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carolin31
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AFNI Message Board
Dear Afni experts,
I am trying to use the @AddEdge program to check the alignment result (aligning functional to anatomical dataset).
I would like AddEdge to show me an overlay of the edges of the final anatomical image and of the edges of the functional image (before alignment). And then the same with the Edges of the functional (after alignment).
The overlays that I get in the AddEdge d
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carolin31
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AFNI Message Board
Hello,
I am trying to use the -AddEdge option to check how good my EPI to anatomy alignment is. Here is my proc.py command that I used. I am using AFNI_17.1.09 on a MacOS.
afni_proc.py -subj_id ${subj}\
-script proc_${subj}.sh\
-out_dir ${top_dir}${subj}/${subj}.${group_id}.preprocessed\
-dsets ${func_dir}obj_test_run1.nii ${func_dir}obj_test_run2.nii ${func_dir}
by
carolin31
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AFNI Message Board
Hi,
I am trying to run 3dDeconvolve with the tent functions. I ran an event related design with a stimulus presentation time of 3 s and an inter stimulus interval of 1 s. My TR is 2.5 and i chose tent (0,12,6). I get the warning:
ESC[7m*+ WARNING:ESC[0m -stim_times 1 .. TENT(0,12,6) has inter-knot TR=2.4 but -iresp output TR=2.5
++ ** GUESSED ** -stim_times 1 using LOCAL times
ESC[7m*+ WA
by
carolin31
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AFNI Message Board
align - 5 years ago
Hi,
I am trying to understand what exactly is happening with the data in the long script generated by afni_proc.py and I have a question regarding the align block.
I used uber_subject.py to generate an afni proc command. I chose among other blocks: align and volreg.
I don t understand a couple things:
1. Why does the afni_proc command (generated by uber_subject) include the option '-
by
carolin31
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AFNI Message Board
Hi Rick,
thank you very much for your reply. Yes, I practiced with the AFNI_data6.
The afni version is afni 18.1.09. It looks like the problem is resolved though. It might have been a permission problem. As other problems followed this GLTsymtest errors. But it looks like a programmer could fix it.
Carolin
by
carolin31
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AFNI Message Board
Hi,
i am new to afni and i am currently trying to learn how to use this program. For practice I would like to use uber_subject.py to generate a script. I encountered the following problem: in the section 'symbolic GLTs', I use the 'init with examples' button to give me some suggestions for contrasts.
When i click later on 'generate script' i get the following err
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carolin31
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AFNI Message Board
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Pages: 12