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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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Hi Rick,
Unfortunately, I don't have physiological recordings, which I guess would have solved all my problems.
I think I will use the 1dBport and 3dDeconvolve to create the X matrix and use 3dTproject to actually regress out the "bad stuff". That way the QC html page would track DoFs correctly.
On that note, I would like to ask the bandpass filter question again:
I hav
by
kausar
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AFNI Message Board
Hi Rick,
I generated the script using afni_proc.py but I have made changes to it. For instance, doing bandpassing is one of them. Instead of generating sinusoidal regressors using 1dBport, I do bandpassing directly using 3dTproject:
3dTproject -polort 0 -input $output_dir/pb05.$SBJ.r*.scale+orig.HEAD \
-censor $output_dir/censor_${SBJ}_combined_2.1D -cenmode ZERO \
by
kausar
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AFNI Message Board
Hi, Paul-
Thanks for the reply. That was a long post by me, I agree. Sorry about that :)
Q2: I had noticed the ~mm thing but I love these little tidbits about AFNI :) I think I agree with you that enorm does the job that it's supposed to be doing.
Q3: Partial volume effect was a concern for me as well, especially with this resolution. So, I am eroding the WM mask by -2 (3dmask_tool
by
kausar
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AFNI Message Board
Dear AFNI experts,
I am processing resting-state data with a script with slight modifications to the one generated by Example 11 from afni_proc.py.
Just for a recap, this pipeline uses, Freesurfer outputs of the T1 and ANATICOR. It doesn't include band-pass filtering but I have added that myself to the pipeline.
I have a few questions related to this pipeline and I was hoping AFNI exp
by
kausar
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AFNI Message Board
I am processing a dataset these days and I was trying to figure out whether to bandpass or not and this discussion was very helpful. I have one main concern:
Considering that I dont have physio recordings, just like samw, what would be a good justification when a reviewer complains about the cardiac and respiratory noise left in the data? It's more of a strategy question but I am asking b
by
kausar
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AFNI Message Board
Hi,
I just updated AFNI on my laptop and tried this command (RBA -help | less) and it failed. In fact, I can't find any scripts named RBA or similar in my AFNI directory. Am I doing something wrong?
This is the output of afni -ver command from 5 mins ago on my computer:
Precompiled binary linux_ubuntu_16_64: Apr 25 2019 (Version AFNI_19.1.06 'Caligula')
Kausar
by
kausar
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AFNI Message Board
Dear Gang,
First of all, thanks for releasing MBA. I have been waiting for this.
I updated my AFNI and ran the command MBA.R | less (MBA | less gives an error "command not found") to see how to use this program and this is what I got:
/home/kabbas/abin/AFNI_Batch_R
R CMD BATCH --no-restore --save --no-readline --vanilla /home/kabbas/abin/MBA.R --args /home/kabbas/abin/MBA.R
by
kausar
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AFNI Message Board
Thanks Zhark. I knew this, I was just wishing it to be wrong :)
-Kausar
by
kausar
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AFNI Message Board
Dear AFNI experts,
I have two groups of resting state data with TRs of 2 and 1.5 sec. I want to compare these two groups. How do I minimize or eliminate the effect of different TRs?
Thanks,
Kausar
by
kausar
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AFNI Message Board
Resampling usually works for me in a situation like this. Did you use your whole brain correlational map as the master dataset while resampling? That would actually put both datasets in the same grid and I think then should not have any problems.
Kausar
by
kausar
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AFNI Message Board
Peter,
Thanks for such a quick reply.
First in order to get the affine and non-linear transformations, I use 3dQwarp:
3dAllineate -prefix anat_SSA -base TT_N27+tlrc \
-source anat_SS+orig -twopass -cost lpa \
-1Dmatrix_save anat_SSA.aff12.1D \
-autoweight -fineblur 3 -cmass
3dQwarp -prefix anat_SSAQ -duplo -us
by
kausar
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AFNI Message Board
Hi Rick,
I have followed these steps to align the epi dataset to the template (TT_N27+tlrc) using 3dQwarp. But, it seems the non-linear transformation does not work. Not only the output epi is not aligned with the template, its shape is stretched in a strange way.
The anatomical I get as the output from 3dQwarp is very very well aligned with the template. But, when I apply the affine and t
by
kausar
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AFNI Message Board
Where can I find that script or the software and if possible, some guidelines to use it properly?
by
kausar
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AFNI Message Board
I am doing the bandpass filtering but that does not take care of the physiological noise, as I understand because most of physiological noise is in the same range of frequency spectrum as the resting state signal.
Thanks,
Kausar
by
kausar
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AFNI Message Board
Hi,
I am doing Resting State (RS) connectivity analysis. Theoretically, any signal in the white matter (WM) should be considered noise. So after regressing out every regressor of no-interest, can I do the connectivity analysis just on the gray matter (GM) ?
Thanks,
Kausar Abbas
by
kausar
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AFNI Message Board
Hi,
I am trying process Resting State (RS) data. One of the steps includes regressing out the physiological noise. RETROCICOR works fine for the subjects for whom I recorded the cardiac and repiratory phase data using external monitoring system during the RS scan. However, for some of the subjects, I don't have that phase data. Is there any way to generate those physiology regressors with
by
kausar
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AFNI Message Board
I forgot to thank you Rick and tell you that it worked.
Thanks,
Kausar Abbas
by
kausar
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AFNI Message Board
Hi,
I was trying to generate a script for the resting state analysis using afni_proc.py on command line. I tried example 10 in the help file of afni_proc.py
It gives me an error for "-mask_segment_anat" and "-regress_ROI". It says "unknown arguments". When I remove these two it works perfectly and generates a script. Here is what I wrote on command line:
af
by
kausar
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AFNI Message Board