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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'll be on the lookout for it then.
I'm sure it would makes lots of people's life much easier!
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ns
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AFNI Message Board
Hi AFNI experts,
is it possible to do multivariate analyses using PLS, based on the approach developed by McIntosh, in AFNI?
I know that it is possible with toolboxes in other software, but I wonder if there is a set of commands or a guide/documentation on how to do it in AFNI.
thanks
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ns
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AFNI Message Board
3dresample worked well. I'm going to follow your suggestion and use afni_proc.py for alignments. thank you
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ns
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AFNI Message Board
thanks, I get now why it wasn't working earlier. I used the the MNI152_T1_2009c template with @auto_tlrc, but when using 3dROIstats later to get the beta coefficient for each voxel/node of the Schaefer_17N_400, I see a message in the terminal saying that my dataset has 8530021 voxels/nodes while the mask has 16777216. am I using the wrong template? thanks
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ns
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AFNI Message Board
hi!
I'd like to use the @auto_tlrc function to standardize my anatomical image to the Schaefer 2018 atlas.
First off, I align the epi to the anatomical image:
align_epi_anat.py -anat "$sub".struc+orig -epi "$sub".image+orig -epi_base 10
and then use @auto_tlrc:
@auto_tlrc -no_ss -base $directory/Schaefer2018_400Parcels_7Networks_order_FSLMNI152_2mm.+tlrc -input
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ns
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AFNI Message Board
I successfully ran ICC(3,1) with a GM mask based on TT_N27 covering the whole brain.
I had issues running ICC(2,1) with a mask covering amygdala and fusiform gyrus.
sub-brik 11contains t-stat for a contrast of interest:
#!/usr/bin/env tcsh
3dICC -prefix ICC2_N40_amyIT. -jobs 2 \
-model '1+(1|session)+(1|Subj)' \
-mask amy.IT_mask.+tlrc. \
-dataTable \
Subj session InputF
by
ns
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AFNI Message Board
Hi AFNI experts,
I'm trying to set up a couple of reliability analyses but there are some details that I'm not sure about.
I'm referring to the HBM paper (https://doi.org/10.1002/hbm.23909) and AFNI documentation on 3dICC (https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dICC.html)
1. I'm trying a whole brain ICC, and I'm then planning to use ICC(3,1). The pa
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ns
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AFNI Message Board
The version that I had was AFNI_19.3.09 (Nero).
With the binaries update, everything works smoothly.
thanks much!
ns
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ns
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AFNI Message Board
Hi,
I'm having issues running @auto_tlrc on a new laptop (never had this issue before). In the attached screenshot, there is a list of files created before it stops
this is what I'm running in my script:
@auto_tlrc -apar ../$sub/$sub.struc_al+tlrc -input $sub.memory.cat.STbeta.+orig -dxyz 2.5
The messages that I see in the terminal:
++ Wrote bucket dataset into ./6475.memory.c
by
ns
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AFNI Message Board
Dear AFNI experts,
I completed a gPPI analysis following the step-by-step tutorial on AFNI website (https://afni.nimh.nih.gov/CD-CorrAna) and I have one question.
After the deconvolution and the t-test between my two conditions (threat and safe), I want to get the beta values for the two conditions for each subject to look at the relationship between functional connectivity and some self repo
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ns
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AFNI Message Board
This is what I get from that command:
N-1 header file 'subj1.nii', num_fields = 43
all fields:
name offset nvals values
------------------- ------ ----- ------
sizeof_hdr 0 1 348
data_type 4 10
db_name 14 18
extents 32 1 0
session_error 36 1
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ns
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AFNI Message Board
I'm trying to read the header of nii files created from a 3T Philips scanner
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ns
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AFNI Message Board
hello,
I'm trying to figure out where I can get the information regarding slice timing in the EPI file.
the -VERB option in 3dinfo doesn't provide this info, and if I try to add -slice_timing I get a series of 0s out.
Any idea of what's happening? I'd like to know from the EPI the acquisition characteristics to use in 3dTshift.
thank you,
ns
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ns
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AFNI Message Board
I didn't consider this huge drawback. then, it's better not to try this analysis with the current data set.
thanks much for the suggestions/advice.
ns
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ns
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AFNI Message Board
thanks, it seems to be exactly what I'm looking for.
How many time points do I need to perform this type of correlation? I have 8 time points per trial, and this is the message that I received when I tried to run it:
ERROR: Input dataset './0128136.CSPLINz.ThreatNoPic.1stHalf.IRF+tlrc.HEAD' is too short: 8 time points
I understand that these type of correlation might be well
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ns
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AFNI Message Board
Hi,
I'd like to perform a global brain connectivity (GBC) analysis and replicate the following procedure described in a paper:
"..first computed GBC maps independently for the safe and threat conditions by correlating each voxel’s timecourse with every other voxel’s timecourse, applying the Fisher’s Z transformation, and averaging across these correlation maps".
The gray matt
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ns
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AFNI Message Board
thank you, I'll try this option to align the child dataset then
ns
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ns
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AFNI Message Board
Hi!
I have 4 axial slices of functional data (5mm x 2.5 x 2.5) that I would like to align to the structural t1 and then tlrc to a standard space (to have ROI references from the atlas that I currently use, TT_N27).
Is there a pipeline to deal with these type of data? any recommendation on how to procede?
thank you,
ns
by
ns
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AFNI Message Board
hi everyone,
I'm interested in using a cerebellar atlas - - with my ANOVA file. However, while the ANOVA file contains info about the whole brain, the cerebellar atlas seems to be just a subsection of the whole space. How can I combine these two type of info?
thanks
ns
by
ns
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AFNI Message Board
Daniel, as you recommended, I used 3dmaskave and 3dTcorr1D for the correlation analysis.
However, I still have a question about 3dfim+. Is there a way to get out the info about the best index (best kth ideal)? I'm wondering if I can get out a txt file containing more info about it.
thanks
ns
by
ns
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AFNI Message Board
Hello AFNI users,
I’m running a correlation analysis using the 3dfim+ command and I have some questions about the ideal function.
I'm currently using the whole amygdala as seed region, resulting in 172 ideals. I read in the 3dfim+ documentation that, when there are multiple ideals, “the kth ideal is referred to as the ‘Best Index’, and the program reports the parameters alpha, p, etc., for
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ns
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AFNI Message Board
Sorry Rich - The attached graphs didn't show what I meant to show.
Attached find 1 image where I have selected one voxel in the visual cortex which had a positive BOLD change (img1.png). Regions with high positive correlations
(red/orange) are depicted in the left side of img1.png and show a positive BOLD waveform. BUT, in the thalamus, regions with positive correlation (red/orange) - the
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ns
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AFNI Message Board
Hi AFNI users,
I'm trying to use - just as exploratory analysis - InstaCorr on the waveforms from BLOCK in 3dDeconvolve..
When I run the InstaCorr on the visual cortex (image 1), the output correctly shows me positive and negative correlations.
When I do the same thing from the thalamus (image 2), negative correlations are shows as positive.
Am I missing something or doing somethin
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ns
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AFNI Message Board
Yes that makes sense. Thanks alot.
One more question, if you don't mind. Let's say we use CSPLIN (3,12,4) and then do a contrast between 2 conditions at one lag. e.g:
+cond1[1] -cond2[1]
Will the coefficient that is printed for the glt at each voxel be the DIFFERENCE of the IRF's for each condition for this at this timepoint?
i.e. will the coefficient = IRF.cond1[1]-IRF
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ns
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AFNI Message Board
And no - there are no errors - just the odd matrix which is impossible to understand?
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ns
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AFNI Message Board
Hmmmm. But the IRF output for CSPLINzero has 6 parameters: the 1st and 6th are 0 and then the are betas are at 1,2,3,4. So- are you saying that in 3dDeconvolve when we specify the "lag" (see below), we are supposed to change from 2..4 to 1..3? That seems OK, but is that documented anywhere do you know? thanks, nicola
So, for instance, following the -gltsym command, we were putting t
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ns
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AFNI Message Board
Hello,
I'm trying to use the gltsym command with 3dDeconvolve to run linear tests between my conditions in different time points.
I don't understand in the output matrix the order and the numbers of the lags. By defining the lags [2..4] I expected to get 3 time points for each variable, and not 4 (as the output suggests).
INPUT:
3dDeconvolve -input r4.$sub.pic.scale+orig.HEAD
by
ns
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AFNI Message Board