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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:
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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 3
Pages: 123
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Thanks Paul, the ROI's are now binary but I'm still getting the same issues of getting the following warning:
*+ WARNING: output sub-brick 0 is all zeros!
when trying to visualize the tracts. Why is that?
by
sondosayyash
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AFNI Message Board
Hi there,
Once I perform probabilistic tractography, I wanted to visualize my tracts using suma
Following the steps on the afni link:
I tried to run the following command
suma \
-vol o.NETS_AND_000_PAIRMAP+orig[0] \
-vol DT_FA+orig \
-vol ../ROI_ICMAP_GMI+orig[0] \
-gdset o.NETS_AND_000.niml.
by
sondosayyash
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AFNI Message Board
Ah, thank you for pointing that out.
I corrected it, and now it now works :)
by
sondosayyash
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AFNI Message Board
Hi there,
I am trying to run 3dTrackID for probabilistic tractography
3dTrackID -mode PROB -dti_in /Users/dti-afni*.nii.gz -netrois /Users/ROIs_GMI.nii.gz -uncert /Users/dti-afni_dwuncert.nii.gz -alg_Thresh_FA 0.2 -alg_Thresh_Frac 0.1 -alg_Nseed_Vox 5 -alg_Nmonte 1000 -prefix network6
However, every time I run this code I get the following error:
** ERROR: Failed to load '-n
by
sondosayyash
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AFNI Message Board
Hi everyone,
I was running a command 3dNetCorr,
And I receive this warning message:
*+ WARNING: THD_Tcorr1D: 16 voxels skipped because were constant in time
I have warning messages for as much as 35 voxels skipped. When I tried to add a mask as an argument to the command 3dNetCorr it actually resulted in more of these warning errors.
For me to resolve the issue, I have to first
by
sondosayyash
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AFNI Message Board
Thanks for the tips, Paul. It really helped. I noticed in the documentation that the brain was split into left and right thalamus, but there were no instructions on how (or why) to do that. When I tried looking it up, most forums suggested to do some additional step in freesurfer. Is there any other way around that?
Also, when I used the fat_proc_connec_vis in the following way:
fat_pro
by
sondosayyash
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AFNI Message Board
Thanks Paul.
So I took a look again, and I figured out why things don't quite look right. It has to do with the 3dTrackID step.
I realized that I got the following error, but did not notice it:
++ Tracking mode: PROB
++ Number of ROIs in netw[0] = 9
++ No refset labeltable for naming things.
++ SEARCHING for vector files with prefix '/Users/dti-afni*':
FINDING:
by
sondosayyash
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AFNI Message Board
Ah, that makes sense. It fixed the problem.
Only now the output I get is quite odd, and I don't think it's correct. I tried looking at FATCAT_DEMO to find something I can compare it against, but I couldn't find it.
I'm not sure if I can email you the files I get as output from 3dTrackID.. I tried to map it onto SUMA and it didn't seem to work out too well (bec
by
sondosayyash
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AFNI Message Board
Hi Paul
Thanks for the clarification :)
I put the Users/ as my directory but that is not the directory I have all my files in. I just did that to simplify the troubleshooting (maybe it ended up causing more confusion).
So now that I fixed the file name for the argument, it ran with no trouble in finding the vector files.
But now I'm getting another error:
SEARCHING for
by
sondosayyash
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AFNI Message Board
Hi everyone,
I've been having a hard time running 3dTrackID. It seems like every time I run it I get the following error:
SEARCHING for vector files with prefix '/Users/dti-afni_DT.nii.gz*':
FINDING: ** FATAL ERROR: Can't open dataset: 'V1' file
My question is... why is the program looking for the vector files in the folder "dti-afni_DT.nii.gz&quo
by
sondosayyash
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AFNI Message Board
Hi Paul
I'm not sure what you mean by 'how many GLT's are there?' wouldn't it run one GLT for all subject?
There are 10 ROI's.
Do you have any suggestions for what I could do to work around this?
by
sondosayyash
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AFNI Message Board
Hi Paul,
the command I used is:
fat_mvm_scripter.py --vars='Subj visit' --log_file=/Users/network3/MVMprep.log --table=/Users/network3/MVMtbl.txt --prefix=study_MVMscripter
Also, I'm working with 794 subjects.
by
sondosayyash
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AFNI Message Board
When I try to run :
tcsh study_MVMscripter_scri.tcsh
which was an output from: fat_mvm_scripter.py
I get the following message:
Argument list too long.
But I'm not sure what to do about that and how to fix it.
Any help would be appreciated.
by
sondosayyash
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AFNI Message Board
Hey there,
So I was trying to use the command: fat_mvm_prep.py from the FATCAT packages.
and I noticed that the input options are:
fat_mvm_prep.py -p PREFIX -c CSV_FILE \\
{ -m MATR_FILES | -l LIST}
but my question is, if I input a a list (as one of the arguments), will the fat_mvm_prep command automaticaLly match each of the subjects in my list to the matc
by
sondosayyash
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AFNI Message Board
Hi everyone,
I was wondering if there was a way to determine the optimal number of ROI's one can achieve from performing 3dROIMaker?
There are many arguments that come with the 3dROIMaker command. And while they are useful, they can be overwhelming in the sense that I'm not sure how to get that golden number of ROI's that are optimal for each network?
Playing around wit
by
sondosayyash
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AFNI Message Board
Hi there,
I was performing 3dMatch, but wanted to look at the folder that is outputted which reports the percentage match between the standard functional template (brain networks) against your data (independent components)
The REF folder looked something like this:
0 5 0.504 0.187
1 8 0.460 0.200
2 3 0.397 0.164
3 4 0.390 0.141
4 17 0.428 0.107
5 10 0.404 0.182
by
sondosayyash
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AFNI Message Board
Thank you for your response.
I see what you're saying but I had questions with both approaches you suggested.
for the first suggestion: 1) from the individual-level results, only keep ROIs that are common across subjects.
I was trying to do that, but I was saying how about in the case where some individual-level results contain fewer number of ROI's compared to the group? Eve
by
sondosayyash
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AFNI Message Board
Hi there,
I am currently using the FATCAT commands in order to combine fmri and dti data.
However, I noticed that after performing the dual regression (on the functional data), in order to get z-score maps at the subject level, each subject contains a different number of ROIs (3dROIMaker step). We don't get the same number of ROI's across all subjects. Do you have any suggestions o
by
sondosayyash
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AFNI Message Board
I was trying to plot the .netcc files produced by 3dNetCorr as a matrix and tried to follow the steps from this link;
I made sure afni and r are installed correctly on my computer.
I even used this command and it ran fine (following the steps from the website): "
@afni_R_package_install -shiny -circos
However, when I try to run this command:
@FATCAT_matplot ~/my_Netcc_files
by
sondosayyash
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AFNI Message Board
Hi,
I've been trying to get 3dNetCorr to work but I keep getting the following error message: **ERROR: Need to load ROIs with >=1 subbrick...
3dNetCorr -inset Users/rs-fMRI/subject_[0-9][0-9][0-9][0-9]_[0][1]_RSfMRI.nii -in_rois /Users/3dROIMaker/3droimaker_subject[0-9][0-9][0-9][0-9]_[0][1]_GM.nii* -fish_z -ts_wb_corr -mask /Users/rs-fMRI/subject_[0-9][0-9][0-9][0-9]_[0][1]_RSfM
by
sondosayyash
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AFNI Message Board
Hi there,
So I had a question.
I have two transformations:
1. T1-weigted image in standard space TRANSFORM
2. T1-weighted to T2-weighted-epi (Diffusion weighted space) TRANSFORM
I transformed these using the flirt and fnirt tool.
But now I would like to concatenate these two transformations together, but inverse both of them before concatenating so I would have the following two t
by
sondosayyash
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AFNI Message Board
Hi everyone,
I've been trying to perform the following command:
3dMatch -inset `cat /Users/sondos/Desktop/dualreg_40subj_output3/directory_dualreg_40subj.txt` -refset /Users/sondos/Desktop/dualreg_40subj_output3/merged_Yeo_40sub_standardSpace_matchingZscore.nii.gz -mask /Users/sondos/Desktop/dualreg_40subj_output3/maskALL.nii.gz -in_min 0 -prefix 3dMatch_40sub
So here, what I'
by
sondosayyash
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AFNI Message Board
3drsfc - 7 years ago
Hello,
I have a question with regards to the afni command 3dRSFC. That is, FATCAT claims that with the command 3dRSFC one can determine the FA between two GM ROI (from fMRI data). However, my question is, how does it obtain the FA from the fMRI data alone? Shouldn't it be combine with the WM regions as well in order to output the FA values?
by
sondosayyash
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AFNI Message Board
Okay, thanks! I will try that :)
I mapped it onto my functional space I believe.
by
sondosayyash
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AFNI Message Board
Hello all,
I have fmri data that I have processed to extract the z-score (or z-threshold) from the independent components. However, now I would like to map these components to DW-native space using an affine transformation via the subjects T1 anatomical image. But I was wondering how I can do that?
Thanks in advance for your help :)
by
sondosayyash
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AFNI Message Board
Hi,
So I had a few questions in regards using the FATCAT toolbox. I
So a little background… Basically, I’m trying to combine resting state fmri with dti (copying the example given in the FATCAT paper but with my own data).
So first off, in the example given in the paper. Spatial ICA is used in native functional space with FSL-melodic.
First question I have from this is how to ru
by
sondosayyash
-
AFNI Message Board
Hi,
So I had a few questions in regards using the FATCAT toolbox. I
So a little background… Basically, I’m trying to combine resting state fmri with dti (copying the example given in the FATCAT paper but with my own data).
So first off, in the example given in the paper. Spatial ICA is used in native functional space with FSL-melodic.
First question I have from this is how to ru
by
sondosayyash
-
AFNI Message Board
Ah, I see. So even though I have multiple subjects, I would have to run 3dRSFC individually on each and then do an in between and group comparison?
by
sondosayyash
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AFNI Message Board
Thank you for your helpful response. Initially I was trying to run it for one subject but realized I should probably try to run it for multiple subjects.
by
sondosayyash
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AFNI Message Board
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Pages: 123