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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 34
Yes, I have a mask block. Here's the command- please let me know if you need more information:
afni_proc.py -subj_id $subj \
-script proc.$subj -scr_overwrite \
-out_dir ${data_dir}/${subj}.${group_id}.preprocessed\
-blocks despike tshift align tlrc volreg blur mask regress \
-copy_anat $data_dir/
by
mmontchal
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AFNI Message Board
I recently ran afni_proc.py, and I noticed that the out.ss_review.txt file no longer includes a line that reports TSNR average for some reason (??). However, the TSNR+tlrc BRIK and HEAD files were still generated. Is there a way to calculate that average from the TSNR maps myself?
by
mmontchal
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AFNI Message Board
using 3dTcorr1D seems to have solved the problem. thank you!
by
mmontchal
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AFNI Message Board
#L nACC
# extract timecourse of L nACC
3dmaskave -quiet -mask ../../Zach_ROIs_onepointfive.nii -mrange 43 44 $1.Entropy.Mood_MOTIONpreprocessed/ANTified_errts_onepointfive.nii.gz > bilat_nACC_timecourse15.txt
#Enforce a TR structure on the data (IMPORTANT!!! Otherwise 3dfim+ in the next step will barf)
3drefit -TR 2.0 $1.Entropy.Mood_MOTIONpreprocessed/ANTified_errts_onepoi
by
mmontchal
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AFNI Message Board
I used afni_proc.py to process my data, followed by registration to a template using ANTS. Data looked normal up until this point. I then ran functional connectivity analysis on the data, including 3dfim+. the images output by this command look like this with some voxels with an Olay value of 0, which doesn't seem right. Does anyone know why that would happen or how to fix it? Thank you.
by
mmontchal
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AFNI Message Board
I have betas from multiple subjects, but I would be doing the correlation within-subject. I want to calculate the correlation of a single-trial beta in one ROI with that of a different ROI within the same subject. Sorry for lack of clarity... I hope that helps
by
mmontchal
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AFNI Message Board
I have single-trial betas. I want to correlate betas in ROI X with those in ROI Y. I saw that functions like 3dNetCorr require a 3d+time dataset. I am looking to get a correlation coefficient as my output. Is there a function for this?
by
mmontchal
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AFNI Message Board
I have some ROIs that I want to view as an overlay on top of a +tlrc template. I currently can't because the ROIs are not +tlrc (they are a .nii file) so AFNI switches the underlay every time I try. The ROIs and template are already aligned, but AFNI just doesn't realize it yet. I ran the following:
@auto_tlrc -base modeltemplate_ns.nii -input Warped_ROIs.nii -no_ss
the output was
by
mmontchal
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AFNI Message Board
how do I restrict it to one value in the mask? My mask has multiple ROIs, but I only want to use one. Like how you can use "mrange" with 3dmaskave
by
mmontchal
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AFNI Message Board
I want to remove null (inactive) voxels from my analysis. I have an ROI mask. I want to restrict my analysis to the top 70% of active voxels within the mask. I have figured out how to use 3dBrickStat to get the numerical value of the 70th percentile of my data. However, I am stuck on how to mask by that. It looks like 3dmerge allows you to use a mask but not to specify a value (mrange) within tha
by
mmontchal
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AFNI Message Board
I'm using afni_proc.py, which removes TRs containing motion events. In the documentation, nothing is mentioned about removing the TR before and after. I would like to include this in my processing. What is the best way to do this?
by
mmontchal
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AFNI Message Board
The latter. I guess I should really describe it as a precision metric. So we want to find regions that are more engaged for trials where there is more precision. and the precision "value" is continuous
by
mmontchal
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AFNI Message Board
What is the best way to run 3dDeconvolve when you have a continuous variable (e.g. error in seconds). Each trial has an error value from 0-1900. I also have baseline trials.
by
mmontchal
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AFNI Message Board
I want to run a 3dmaskave call on two ROIs whose numerical labels aren't next to each other (so I don't think -mrange would work) I'm trying to combine anterior/posterior hippocampal ROIs. so for example the posterior hippocampus is 13 and the anterior hippocampus is 19, and I want to combine them to make a full hippocampus ROI.
Is there a way to do this without making new ROI
by
mmontchal
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AFNI Message Board
To be clear, I was trying to run 3dmaskave on chunks of slices in the anterior to posterior dimension. I didn't want LTR or inferior to superior slices, so I reoriented the data. I didn't realize that slices are in the z-dimension by default. so I made anterior/posterior the z dimension and then ran 3dmaskave. thanks for your help!
by
mmontchal
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AFNI Message Board
to my knowledge I haven't resampled/reoriented the data. Here is the orientation info when I 3dinfo my data:
Data Axes Tilt: Plumb
Data Axes Orientation:
first (x) = Anterior-to-Posterior
second (y) = Superior-to-Inferior
third (z) = Left-to-Right [-orient ASL]
Is that what you would expect?
I'm confused about how to determine which slices I want. When the z-value
by
mmontchal
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AFNI Message Board
I want to get an average beta value for each slice along an ROI. I saw that 3dmaskave's -slice option only goes in the z-direction, but in my data slices are in the y-direction. I am currently trying to do it using 3dmaskdump, but that gives me many betas and I would need to average them afterwards. Is there a better way to do this? this is my current 3dmaskdump command to get values from wh
by
mmontchal
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AFNI Message Board
after nudging a dataset, it loads into AFNI as orange by default. whereas before, it was green. does this indicate a problem or is it normal?
by
mmontchal
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AFNI Message Board
I just tried again and it worked! I'm not sure what the issue was (could be as simple as not saving the file before running the command). thank you for all your help!
by
mmontchal
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AFNI Message Board
I'm having difficulty figuring out what I'm doing wrong. I'm getting the following output/error:
++ '-stim_times_AM1 1 stimuli/happy.1D' has 1 auxiliary values per time point
++ '-stim_times_AM1 1': basis function model 'dmBLOCK' uses 1 parameters,
out of the 1 found in timing file 'stimuli/happy.1D'
++ '-stim_times_AM1 2 sti
by
mmontchal
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AFNI Message Board
Thanks! How would I implement this with afni_proc.py?
This is my current call:
afni_proc.py -subj_id ${subj}\
-check_results_dir no\
-script proc_${subj}_AF_new.sh\
-out_dir ${top_dir}${subj}/${subj}.${group_id}.preprocessed\
-dsets ${func_dir}raw_run1+orig.HEAD \
-blocks tshift despike align volreg blur mask regress\
-copy_anat ${struct_dir}struct_ns+orig.HEAD\
-anat_has_sku
by
mmontchal
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AFNI Message Board
yes. The documentation says to use '-stim_times_AM1' with dmBLOCK, but I don't see an example of that. Would the stim times files be a series of onset times and duration like this: 30.43:1.2 ? with 30.43 as the onset time and 1.2 as the duration? or is it more complicated than that?
by
mmontchal
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AFNI Message Board
I'm getting an error when trying to run 3dDetrend on time series data. I got the following error:
++ 3dDetrend: AFNI version=AFNI_16.0.10 (Feb 25 2016) [64-bit]
*** Illegal inputs to startup_lsqfit
** FATAL ERROR: Choleski factorization fails: linearly dependent vectors!
this is my 3dDetrend call:
3dDetrend -polort 1 -prefix detrend_run1_101_RHead_Sub run1_101_RHead_Sub.1D
My in
by
mmontchal
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AFNI Message Board
you're right-- I do want 7 tents. thanks!
I was referring to whatever the numbers after "num TRs per stim (orig)" refer to. It was my understanding that they're conditions (the first 3 are the conditions I specified and the rest are motion regressors etc). Is that true? I understand what you're saying about the tents, but I'm still not clear on why this would diff
by
mmontchal
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AFNI Message Board
My TR is 2.5s, and my events are not TR-locked for any condition. My conditions are determined by participants' performance, so there are no differences between them in terms of TR locking. This is a big part of why I am so baffled by this issue.
Here is a link to a zipped folder with my proc_101.sh script, output, and stim times files in case that helps you:
thank you for your help a
by
mmontchal
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AFNI Message Board
the basis functions are the same ('TENT(0,15,6)') for all regressors.
I don't think this can be explained by having events in this condition happen at the very end of the runs. I time my experiments so that I have 1-2s of scanning after the task ends. Additionally, the difference is very large (~30 vs ~60 TRs). and it's consistent for all of my participants. I just double c
by
mmontchal
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AFNI Message Board
thanks, that's really helpful!
I have a followup question. I'm guessing the regressors are ordered in the same way as in proc_###.sh. In my case, that's the first 3. All of my regressors have the same # of stimulus onset times. However, in the "num TRs per stim (orig)" field, my first regressor consistently has many fewer TRs than the others, even though it has the sam
by
mmontchal
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AFNI Message Board
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Pages: 12