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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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I have my own .par file from MELODIC, but I was wondering how I can use it in the afni_proc.py command? FSL's MELODIC outputs a .par file, which contains all the motion parameters. I want to regress out these motion parameters. So I'm not sure how to incorporate that into afni_proc.py . Do I need to change the file type to a 1D?
Here's an example code of what I expect to run:
by
sondosayyash
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AFNI Message Board
Yes I was going to use DTI-defined white matter to create the tissue type. Would that be okay?
I can also look into freesurfer, but I was just wondering if it would make sense to use the 3dROIMaker, where I can filter out CSF and white matter. I don't see how much different that would be.
by
sondosayyash
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AFNI Message Board
Hi there,
I've noticed that some resting-state preprocessing pipelines include regressing out signal from the white matter and CSF. However, I'm wondering if this is a necessary step in FATCATs 3dROIMaker, if we select the "trim_off_wm" ? It seems to me that in a sense, that is regressing out the signal.
What are your thoughts?
by
sondosayyash
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AFNI Message Board
Hi there,
I'm wondering how I can extract the MNI coordinates of my ROIs. Each ROI is labelled with an integer value, which was output from 3dROIMaker.
I'm not sure if there's a command to help me do that.
Thank you so much for your time!
by
sondosayyash
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AFNI Message Board
Thanks Paul, I'll have a look at these resources :)
And thank you Rick for your feedback :) that makes sense.
I realize now that the errts files are the final output for resting state from uber_subject.py .
The reason I was running my data through subject_proc.py first is because I wanted to preprocess my functional data with afni prior to applying ICA (with FSL) on my data.
by
sondosayyash
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AFNI Message Board
Thanks Paul,
Correct me if I'm wrong but I thought all the motion stuff will be output into errts, and that it's not the final preprocessed version of my functional data. Even when I open it up on my computer it looks like a bunch of noise and not a functional brain image.
I'm just not sure how I get the final version of my preprocessed data, if that makes sense.
by
sondosayyash
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AFNI Message Board
Hi everyone
So I've been running my 4d resting state functional data in uber_subject.py and what I've noticed is that once it's done running it outputs a 1D file called final_epi_vr_base+tlrc. The functional data I originally input however, had 108 volumes (functional data) but the preprocessed output from uber_sujbect.py only has one volume. I'm wondering why that is an
by
sondosayyash
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AFNI Message Board
Everytime I run uber_subject.py it changes my pixdim4 from a 3 to a zero.. I'm not sure why this happens but it causes me trouble in my next analysis steps.. is there some way I can overcome this issue?
by
sondosayyash
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AFNI Message Board
Hi there,
So I understand how to perform uber_subject.py for one subject but I’m wondering how I can now do it for a group of subjects?
Let’s say I have subject 1...100 and I want to preprocess all of them with uber_subjects.py. How can I do that?
Any help or guidance would be appreciated.
Thanks for your time.
by
sondosayyash
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AFNI Message Board
uber_subj.py
Can I enter my own standard T1 template instead of the standard MNI152 into uber_subj.py?
by
sondosayyash
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AFNI Message Board
Hi there,
I have resting-state fMRI images for children data and wanted to preprocess them using the afni_proc.py code. However, I was getting really confused as to which example I should follow since there's about 7 examples for resting state. It got really overwhelming, with a lot of technical detail, so I was hoping to get some insight into which example might best suite my applicat
by
sondosayyash
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AFNI Message Board
Hi everyone,
I'm trying to read the dicom headers and everytime I use this command I get the following crash error:
Fatal Signal 11 (SIGSEGV) received
Last STATUS: DCM_OpenFile open failed; try again as Part 10
mri_dicom_header
dicom_hdr main
Bottom of Debug Stack
** AFNI version = AFNI_18.0.22 Compile date = Feb 26 2018
** []
** Program Death **
** If you report this
by
sondosayyash
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AFNI Message Board
Hi everyone,
I'm wondering if there is a standard way to obtain the fieldmap images? I have my structural (T1 weighted images) and DTI images and fMRI images.
My scans were obtained using a GE scanner. I was wondering if there was some command to allow me to obtain the fieldmap images so I can use it for preprocessing my data?
Any help would be greatly appreciated.
Thank you
by
sondosayyash
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AFNI Message Board
That makes sense.
But I'm not interested in all tracts that pass through ROI1,
I'm interested in getting the maximum number of tracks starting at ROI1 and leaving it (whether it goes through a target or not)
by
sondosayyash
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AFNI Message Board
Hi Paul, I hope you're doing well.
I wanted to follow up on this.
how can I get the maximum number of tracts leaving an ROI?
I know the number of tracts running between two ROIs is stored in the .grid file as NT.
However, I'm interested in the total number of tracts leaving ROI1 for instance (whether it reaches a target or not).
How can I get this information?
From
by
sondosayyash
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AFNI Message Board
Ah, okay thank you for providing that very insightful and clear explanation as to what's going on.
I was using functional ROI's at the 3dMatch step, and the majority of my ROI's are already quite large. I can see how it might be problematic to inflate too much.
Oh, I also noticed that for the 3dTrackID step I was inputting the alg_Thresh_Frac to 0.1(now I can't seem to
by
sondosayyash
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AFNI Message Board
Would it be wrong to have 0 number of tracts running between 2 ROIs? The grid output will sometimes return a #NT of zero between two ROIs. That implies that there are no structural connections running between a set of ROIs. I know some ROIs are connected through indirect structural connections, but is that the case for ROIs that are not expanded far enough to touch the white matter?
I'
by
sondosayyash
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AFNI Message Board
Hi everyone,
I'm not sure if anyone would be able to help me out with this.
But here it goes:
I have a functional connectivity (correlation coefficient) matrix derived from fMRI . I have 5 Networks I'm looking at (i.e. DMN, FPN, SN, etc) - each of which have 10 ROIs'.
When I want to do a statistical analysis I don't want to do an ROI-ROI t-test and then a post hoc
by
sondosayyash
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AFNI Message Board
Hi again,
Now that I checked the grid files again, there are actually ROI's missing and they don't show up.
For example if its 5 ROI's, ROI 1 might not show up at all, and this can be computationally complicated.
However, in the case of 3dNetCorr all ROI's are present and have values in the matrix.
So does that mean that there is a funcitonal correlation and no structu
by
sondosayyash
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AFNI Message Board
Hi AFNI experts,
So I have a slightly complicated problem, which I'm hoping I can get help solving.
I've been using FATCAT to perform my functional connectivity analysis, however, when I get to the statistics part (3dMVM) I get errors. It seems that I can't perform this on a large dataset.
To give you an idea of my dataset: I have 750 subjects that I'm studying and
by
sondosayyash
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AFNI Message Board
Hi there,
I've run my 3dNetCorr command. Every time I run it I get a warning error 290 voxels skipped because they were constant in time (or some large value).
So after reading the documentation I realized this is probably because I'm not masking my ROI's correctly. So after I ran melodic.. from the output I got "mean.nii.gz" I did brain extraction tool (BET) to g
by
sondosayyash
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AFNI Message Board
Hi there,
I was trying to determine the maximum number of streams that run between each pair of ROI's.
Would be the right way to go about it:
1) Count the number of voxels from the source ROI (aka seed ROI)
2) Multiply the count by 5 (5 being the default number of seeds/voxel)
Or is this approach wrong?
The way I understand it is that the way Monte-Carlo works is by gener
by
sondosayyash
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AFNI Message Board
The thing about the grid files is that there is information on the number of tracts, fractional number of tracts, physcial volume of tracts, etc but we are not given probabilities of connectivity between each ROI region. I was expecting that maybe FATCAT would output the probabilities of SC between each pair of brain regions.
But I guess what you're saying is: the file.niml.dset does c
by
sondosayyash
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AFNI Message Board
Hi there,
I just finished running 3dTrackID. And wanted to analyze the data. However, now what I wanted to do is to analyze the probabilistic tracts (probability of a path) running from one ROI to another.
I read in the documentation online for this command that the FILE.niml.dset contains the matrix information on the connectivity.
When I looked at the file I couldn't understand t
by
sondosayyash
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AFNI Message Board
Yes, exactly. They showed up as 0's (zeros) in the grid file
by
sondosayyash
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AFNI Message Board
Hi there,
I was taking a look at my 3dtrackID output when I noticed that there is a file missing. I have 5 ROI's in total, however I believe there should be a file titled ROI_001_002 and that does not exist.
I'm not sure what the reasoning for that is exactly. I've attached the 3dtrackid output files if you'd like to take a look at them.
I've attached the ROI&
by
sondosayyash
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AFNI Message Board
I ended up adding an extra argument, -vol GMI_ROIs. I'm not sure if this is correct but it seemed to give me the output I was looking for
by
sondosayyash
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AFNI Message Board
Hi everyone,
I was hoping I can get some clarification on two things.
First is: I was taking a look at the output "PAIRMAP" after running 3dtrackID -mode prob
and I noticed that the tracts are not necessarily continuous and connected between a pair of ROI's.
I've attached an image of what I mean. Is this normal? I thought the way probabilistic tractography works
by
sondosayyash
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AFNI Message Board
I used the fat_proc_connec_vis command in the following way:
fat_proc_connec_vis -in_rois /Users/NET_000_ROI_GMI.nii.gz -prefix testing -trackid_no_or
and I got the following error messages:
*+ WARNING: output sub-brick 0 is all zeros!
What does this mean ?
*+ WARNING: Set TR of output dataset to 1.0 s
++ elapsed time = 0.1 s
Also this confused me.
by
sondosayyash
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AFNI Message Board
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Pages: 123