Show all posts by user
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
Page 1 of 1 Pages: 1
Results 1 - 17 of 17
Thank you very much for your answer.
Would you please tell me how can I extract each ROI signal? (The mean time series of every voxel within the atlas)
by
heretic133
-
AFNI Message Board
Hi everybody
I have read a paper on functional connectivity, and in this paper with the help of SPM and DPARSFA, the author wrapped the brain into AAL atlas and then extracted the ROI signals from these regions.
My question is that how can I do the same using afni. The first thing that I need to do(after preprocessing steps like head motion correction and . . . ) is to wrap the brain into AA
by
heretic133
-
AFNI Message Board
Hi Everyone
I am trying to do classification of rs-fMRI data, The problem is that I have several rs-fMRI data for each person and I have to choose one among them (supposing that they all passed pre-processing steps) but I don't know how. I looked at the data that is left over by uber_subject.py, And I saw TSNR, When I checked the data carefully I saw that usually TSNR average, is correl
by
heretic133
-
AFNI Message Board
Dear rick
Thank you very much for your answer. Using your suggestion I found that I have accidentally added some corrupted masks into my folder. But now I get lots of errors like this:
*+ WARNING: grid from dset full_mask.S211480 does not match that of dset zyxt
Almost all of the rows are identical, except for a few that differ. And the difference is very little :
full_mask.S175640 -3.3
by
heretic133
-
AFNI Message Board
I have several objects and I used uber_subject.py for each one of them. Now I want to get the union of the full_masks created by uber_subject.py.
I have gathered all my masks in a single folder and I then use this command:
3dmask_tool -inputs full_mask.*+orig.HEAD -union -prefix result_mask
But I get this error:
++ processing 110 input datasets...
++ padding all datasets by 0 (for
by
heretic133
-
AFNI Message Board
Thank you very much for your answer.
I created the mask that I wanted.
And the example helped me a lot.
by
heretic133
-
AFNI Message Board
Hello everyone
I have several subjects (around 200) and I used uber_subject.py to do the pre-processing steps on them. In the result folder there are several files that have the mask word in their names, the names are:
rm.mask_r01+orig.HEAD
rm.mask_r01+orig.BRIK.gz
full_mask.S142290+orig.HEAD
full_mask.S142290+orig.BRIK.gz
first of all I would like to know the difference between these fi
by
heretic133
-
AFNI Message Board
Hi
I am using 3dmaskdump -o out.txt -quiet all_runs.a+orig.HEAD to extract the time series for each voxel. The procedure works fine and it generates a very large file. But I'm almost sure that non-brain parts are also included in this file, Because each picture has the dimension 64*64 and I have 48 slices. 3dmaskdump also extract time series for 196608 voxels.
Is there a way to exclude th
by
heretic133
-
AFNI Message Board
Hi
I'm using uber_subject.py to preprocess my resting-state data.
There is an option in expected options section called 'motion censor limit' which is 0.2 by default. I can't fully understand this option. If I'm not wrong, 3dvolreg is used for head motion correction. So if the head motions are handled via 3dvolreg, what is the usage of motion censor limit.
And my othe
by
heretic133
-
AFNI Message Board
Hi
I have several .nii files for a single object and I'm trying to put them in a single file. When I use
3dTcat -tr 3.0 -prefix output+orig *.nii
everything works fine and the program generates 2 files for me. But I have two questions:
1: My slices are interleaved, how can I specify it in 3dTcat? I know that I should use something like this " fred+orig[0..$(2),1..$(2)] " but
by
heretic133
-
AFNI Message Board
Thank you very much.
There is one more question, I am using ADNI dataset and in ADNI the slices are interleaved. Is it something that I should worry about when I'm using 3dTcat?
by
heretic133
-
AFNI Message Board
Thank you very much Bob Cox, I am new to fMRI data processing and Im sorry if my question was vague. I will try to explain more details.
By voxel-wise analysis I mean that every single voxel should be considered as a ROI. you can find more details in this article. As far as I know common approaches tend to find seed voxels or find the ROIs via atlases. But in this approach each single voxel i
by
heretic133
-
AFNI Message Board
I know it may sound silly, But I don't know where to use 3dTcat -TR XXXX -prefix run1 volume*.nii.gz, I tried to copy and paste it in my command line, But it did not work.
And my second problem is that when I open mu subject description the TR looks like this : "TR">3000.0, But for an other patient it is: "TR">3000.9983, Should I use only 3 in my code or I should s
by
heretic133
-
AFNI Message Board
Hi
I'm trying to do the voxel-wise analysis to my data but I don't know the steps.
I have a raw .nii file that contains my rs-fMRI data for a subject.
There are some standard preprocessing steps (Like slice timing, Head motion correction and . . . ) that should be done in general, but I have heard that in voxel-wise processing some of these preprocessing should not be done.
My
by
heretic133
-
AFNI Message Board
Thank you very much, I guess I should read the manual more carefully.
by
heretic133
-
AFNI Message Board
This is exactly what I do:
1) I run uber_subject.py
2) In Analysis Initialization, I choose resting state and apply the changes
3) Since I don't have any anatomical dataset (I just have 141 .nii files for each subject), I uncheck Anatomical Dataset
4) In EPI Datasets section, I load all .nii files
5) Then I generate the cods and run them.
Then I get several warnings and this erro
by
heretic133
-
AFNI Message Board
Hi
I have downloaded ADNI rs-fMRI dataset. Each subject consist of 141 .nii files. I don't know how can I use this files in uber_subject.py. I watched a video on how to process resting state data and in that video the instructor used a single .nii.gz file. I was wondering if there is a way in AFNI to create such .nii.gz file.
by
heretic133
-
AFNI Message Board