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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
I'm having a very similar issue to lsmorris.
I try running suma (either with just "suma" or after opening "afni -niml" with suma -spec MNI_N27_both.spec -sv MNI_N27_SurfVol.nii)
I get warning---------
trying lame single buffer visual
++ Notice SUMA_XtWarn_handler (SUMA_display.c:4114 @11:12:13):
X11 Warning 1:trying lame single buffer visual
Have 1
by
Kirk
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AFNI Message Board
Hi
A colleague of mine pointed me to 3drefit to 'nudge' the mask.
I used:
3drefit -dxorigin 1x File+orig.
This still doesn't seem to work the way I expect it to though.
Can anyone help with this?
by
Kirk
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AFNI Message Board
Hi!
I'm noticing that after downsampling my mask it must have rounded up for both left and right hemispheres. The result is that they are both shifted so my mask for my left hemisphere is in the midline of the brain and the mask for the right hemisphere is too far from the midline. Could you please help me with either
a) How to shift the mask over 1 voxel in the L-R direction. Presuma
by
Kirk
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AFNI Message Board
Hi Gang,
Previously the posted link wasn't working for me so sorry if that already answered my question.
It seems like the 3dsynthesize step is for a pipeline that only works with 1 task or resting state, and because I want to compare two tasks that I should use PPI/Context-Dependent Correlation Analysis. Is that correct?
Thanks so much
Kirk
by
Kirk
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AFNI Message Board
Hi Gang,
I'm doing something similar to above but was hoping for advice on questions I have.
>3dSynthesize -cbucket CbucketFileFrom3dDeconvolve+orig -matrix x1DFrom3dDeconvolve -select ... prefix EffectsOfNoInterest
>Then remove the effects of no interest from the original signal by using 3dcalc:
>3dcalc -a InputFor3Deconvolve -b EffectsOfNoInterest -expr 'a
by
Kirk
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AFNI Message Board
Hi
Thank you so much for your reply.
I was able to update AFNI but I still receive the same error.
It would make sense that the program has issues with modelling stimuli lists that are empty. However I'm not sure what to do about this.
My goal is to model "correct" and "incorrect" trials. However the reason I am including these other trial types (ex. NoResp
by
Kirk
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AFNI Message Board
Hi!
I'm getting the same error but on Afni 2012. I'm not sure I understand what the bug was or how it was fixed.
I posted about it just now here:
Thanks for any advice you can offer
by
Kirk
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AFNI Message Board
HI Afni gurus!
I am getting a Signal 11 (SIGSEGV) error when trying to run 3dDeconvolve (on only some of my subjects).
Here is my script with 3dDecon command.
for i in {1004..1004} #{1007..1008} {1012..1012} {1014..1014} {1023..1023} {1026..1028} # {1023..1023}
do
value=$(<../${i}/GLM_BASIC/scans.txt)
set $value
/home/bradley/bin/qexec2.R -q bigmem_16.q --mem=16G \
3dDecon
by
Kirk
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AFNI Message Board
Hi
So I think I've figured out that the residuals files that are output are 4d. So I'll need to use a warping script that expects this (although it will take a very long time).
So if anyone else is wondering how to warp their residuals files to do 3dClustSim in the same space as their stats were warped, you'll likely need the same.
by
Kirk
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AFNI Message Board
Hi!
I am trying to determine the Cluster size threshold using 3dClustSim (updated process).
My process so far has been to use the same 3ddeconvolve.sh script for each subject as for my main data analysis but with the "-errts residuals" option added.
I then warp and smooth the output residuals+orig. to match my main data analysis.
However at this stage I run into issues. The
by
Kirk
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AFNI Message Board
I just tried
3dcalc -a FILENAME -expr 'step(a-40)' -prefix NEWMASK
And it seems to have worked. Don't know if that helps anyone!
by
Kirk
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AFNI Message Board
Hi,
Is there a way to binarize based on a non-zero threshold? Ex. all voxels with a value of 40 or above -> 1 and below 40 -> 0?
Thanks!
Kirk
by
Kirk
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AFNI Message Board
Okay!
So I am trying out more things with the align_epi_anat.py script. I have tried 3dcopying the anatomy files from /opt/afni/ to my working directory. I have also tried adding -cost lpa (which supposedly estimates transforms better when going from anatomy to anatomy).
It's running now and the result is... "Finished alignment successfully"!!!
Great, thank you so much f
by
Kirk
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AFNI Message Board
Hi Daniel
Unfortunately the atlases by the Zilles group does not have ROIs for the thalamic subregions that I need.
So, I am trying to warp the TT_Daemon atlases into MNI space to get MNI ROIs that way.
My plan is to warp from the afni directory the TT_avg152T1+tlrc.BRIK.gz to the MNI_avg152T1+tlrc.BRIK.gz template. Then I will use the resulting transformation matrix to transform the a
by
Kirk
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AFNI Message Board
Hi Rick,
Unfortunately that is leading to the same warnings I was obtaining earlier (example below. After 288 of these shuts itself down as I haven't been using "GOFORIT").
*+ WARNING: !! * Columns 607 and 703 are nearly collinear!
From what I have described above am I on the right track or do you think there is something fundamentally wrong with what I am trying to do?
by
Kirk
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AFNI Message Board
Hi Rick,
Thanks! Unfortunately this still throws so many warnings that 3dDeconvolve can't run without "-GOFORIT". The warnings may look different this time (although there are so many I'm not sure what all of them said last time). The warnings say "run#x has y times outside range 0 .. 345 and "column x is all zeros, and that the columns are "nearly colline
by
Kirk
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AFNI Message Board
Okay I see.
Yes I agree number of subjects should be irrelevant at this point.
The experiment works by showing 48 scene face pairings, and testing 1/3 of these scenes (16 test trials). This is repeated over 6 blocks.
So 96 is actually the number of trials tested total (16 * 6 blocks).
The different conditions are moderately complicated (and could be simplified somewhat if need be). The
by
Kirk
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AFNI Message Board
Hi Dr. Cox,
Just writing to see if you had further tips on this matter.
Afni is giving me warnings (following) ensuring I really know what I am doing. However I am not entirely sure that is the case. I am getting a lot of warnings about high co-linearity. So perhaps I have this set up wrong?
Thanks for any help you can offer!
WARNING: +++++ !! Matrix inverse average error = 0.00
by
Kirk
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AFNI Message Board
Hi Bob,
Thank you for your reply.
I'm not sure I understand. Each event (time in the stim_times_IM) file is the onset time for a trial under which that condition is true.
Ex. run 1 at 14.1 seconds, 18.2 seconds and so on, marks the start of the study phase for trials that the participant gives the correct response.
To do Beta correlations don't I need to create one Beta pe
by
Kirk
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AFNI Message Board
However, I did get another error.
*+ WARNING: +++++ !! Matrix inverse average error = 0.00115008 ** BEWARE **
++ Matrix setup time = 1870.44 s
** ERROR: !! 3dDeconvolve: Can't run past 288 matrix warnings without '-GOFORIT 288'
** ERROR: !! Currently at -GOFORIT 0
** ERROR: !! See file 3dDeconvolve.err for all WARNING and ERROR messages !!
** ERROR: !! Be s
by
Kirk
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AFNI Message Board
Okay. I see now that the error was because there was no space between the stim_label name and the \.
by
Kirk
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AFNI Message Board
Hi!
I am trying to do Beta correlation analysis (functional connectivity) but I seem to be stuck on the 3dDeconvolve part. I have been using as guides Andy Jahn's youtube tutorial (https://www.youtube.com/watch?v=GNL30C9lyUQ) and an afni wiki (http://polaris.ssc.uwo.ca/mediawiki/index.php/AFNI_single_subject_stats#Multiple_Runs).
I have 17 conditions (ex. study phase + correct, study
by
Kirk
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AFNI Message Board
Okay Thank you very much for the atlas.
The MNI atlas should be exactly what I need. I'll try implementing it and then update on my progress!
by
Kirk
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AFNI Message Board
Hi everyone!
First time posting. I have what feels like a fairly basic question but I can't find simple answers to.
I have fMRI data in MNI space (which I like because I prefer MNI to Talaraich). However the only way I know how to make Regions of Interest /masks from an atlas was to use the TT_Daemon atlas already in afni.
My goal is to either a) learn how to transform masks from TT
by
Kirk
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AFNI Message Board