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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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Paul,
Thanks for the feedback. If I were to use those scans just to analyze the effects on the overall group results, is there a way to specify the run concatenation in afni_proc, or through some other combination of AFNI tools to perform the appropriate pre-processing?
G
by
gsudre
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AFNI Message Board
Hello,
I have two resting state runs for the same subject, but when I pass them to afni_proc using -dsets rest* neither of them have enough TRs after censoring to run 3dDeconvolve. There's a chance I'd have enough TRs if 3dDeconvolve were run on a concatenated time series. (this is a generic description - we have several subjects in such scenario and the number of TRs left after cens
by
gsudre
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AFNI Message Board
Hello,
I see that in the AFNI GUI we can define the value that will be mapped to the highest color (i.e. to 1), but is there a way to map a user-specified value X to zero? I'd like to be able to use the full color-scale after I set a threshold, but I cannot find a way to do that other than using 3dcalc to remove the values below X.
I feel like I'm missing something obvious here..
by
gsudre
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AFNI Message Board
Hello,
Is there a way to overlap results in SUMA? For example, say I have result1 that I want to show in the inflated surface using a yellow-red color scale, and result2, which I want to be showed in the same brain simultaneously in a blue-green color scale.
Is that possible?
Thank you,
Gustavo
by
gsudre
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AFNI Message Board
Hello,
I was wondering if I could get some help with the parameters for slow_surf_clustsim.py?
I'm doing a somewhat basic surface area analysis using values extracted from Freesurfer. After extracting surface area values for each subject/vertex morphed to fsaverage, I get a file I called lh.area.00.mgh. Then, I smooth it using mri_surf2surf and FWHM=10, which results in lh.area.10.mgh.
by
gsudre
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AFNI Message Board
Gang,
Thanks for this info. I tried both methods above to do a T-test between groups X and Y using the PPI effect of conditionA - conditionB.
I was wondering if you could elaborate on the differences between using method 1 (or 2, since they're equivalent), and adding something like:
-gltsym 'SYM: condA -condB' -glt_label 1 condA_vs_condB
to the 3dDeconvolve call for
by
gsudre
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AFNI Message Board
Hello,
I recently updated afni to make use of the pediatric template, and it looks like my afni_proc.py is breaking. Here's the output:
===
#Script is running (command trimmed):
3dNwarpApply -nwarp ./anat.aff.qw_WARP.nii -master ./base.nii -affter anat.aff.Xat.1D -source /XXXpathXXX/mprage_unif_ns+orig -prefix ./mprage_unif_ns.aw.nii
++ 3dNwarpApply: AFNI version=AFNI_2011_12_2
by
gsudre
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AFNI Message Board
Hello,
I'm trying to conduct a simple regression analysis, normally conducted using 3dRegAna, but using 3dttest++. Could anyone help? In 3dRegAna, it looks something like:
3dRegAna –rows 8 -cols 3 -xydata 11 5 32 subject001/glm_out_5mm+tlrc[4] -xydata 8 8 21 subject002/glm_out_5mm+tlrc[4]
-xydata 1 4 43 subject003/glm_out_5mm+tlrc[4] .... -model 1:0 2 3
In other words, I'm u
by
gsudre
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AFNI Message Board
Daniel,
In that case, when editing the resulting 1D, is it as easy as removing the columns that correspond to the dummy physio file, or should I be aware of any other caveats?
Thanks,
g
by
gsudre
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AFNI Message Board
Hello,
Is there a way to run RetroTS (more specifically, the compiled version) with just one type of physiological recording (i.e. either respiration or EKG)? Another solution would be to enter a toy recording for the missing type and just remove the appropriate regressors later in the 1D file, but I wanted to make sure there wasn't an easier way to do that.
For background information,
by
gsudre
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AFNI Message Board
Hello,
I have 2 echo planar datasets (51 time slices each) which need to be interleaved "anatomically". In other words, the two series need to be merged with interleaved slices, and the second series could be shifted up or down. I was playing with 3dcat, but that seems to concatenate them "in time". Any suggestions?
Also, what types of alignment issues should I worry ab
by
gsudre
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AFNI Message Board
Oops, my bad. Didn't know the input to McRetroTS was in Hz, and somehow I had 1dplot in mind while using 1d_tool! It works now. Thanks for the help!
Best,
G
PS: hey, it was a simple question after all! :)
by
gsudre
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AFNI Message Board
Rick,
Thanks for the prompt reply! I think it's something wrong with the output of McRetroTs, because 1d_tool.py fails to parse it.
$ 1d_tool.py -show_rows_cols oba.slibase.1D
** error: unknown trailing arguments : ['oba.slibase.1D']
(the input files have 15750 lines each).
I don't know the specifics of the output file format, but it looks OK to me (322 lines, bu
by
gsudre
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AFNI Message Board
Hello,
I have hopefully a simple question. I'm not removing any TRs from my EPI data, nor removing samples from my physiological data (i.e. no -ricor_regs_nfirst/-tcat_remove_first_trs used). My physiological data has 15750 samples, acquired at 20 ms, so that matches the length of the data (315 s). What other possible mistakes should I check to find out why I'm getting the error mess
by
gsudre
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AFNI Message Board
Hello,
Any chance that you could post the compiled version of retroTS for Mac 64 bits? The current (Intel 32) version is freezing up on 10.8.2 and I'm wondering if that could be the cause...
Thanks,
Gustavo
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gsudre
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AFNI Message Board
Steve and Isaac,
Thanks for the clear responses. I'll let you know if I run into other issues...
Best,
G
by
gsudre
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AFNI Message Board
Hello,
I'm new to AFNI and I have recently inherited a good amount of resting state fMRI data. I'm trying to replicate the analysis in Gotts et al. 2012, and the data was acquired at NIH. I do have physiological data for most of the subjects, and plan to use RetroTS to obtain regressors.
After visually checking some of the .1D files for respiratory and EKG data, some of them look
by
gsudre
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AFNI Message Board