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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 everyone,
I wanted to generate a group mask (an ROI) based on the functional group activations.
I was thinking of using the 3dclusterize command However my cluster of interest does not show up there (actually looking from the GUI report) . It's strange cause its' a big cluster.
Editing: it actually shows up I see it when I click on the Flash option but as en entire huge clus
by
Lysianne
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AFNI Message Board
oh ok then I guess I will first convert to NIFTI format and then probably use a 3dcalc command
by
Lysianne
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AFNI Message Board
Hi you all,
I would like to know whether there is an AFNI command that will allow me subtracting 2 raw DICOM acquisitions?
Thank you!
by
Lysianne
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AFNI Message Board
Like too strong to be correct
hm the color bars are not the same actually, I just let the default set them up
the one without the covariate has a max at 2.027
the one with the covariate has a max of 3.26
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Lysianne
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AFNI Message Board
oh, I haven't look at that before , is it because the posterior brain areas were not sufficiently activated ?
by
Lysianne
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AFNI Message Board
Hello,
I'm emailing you cause I have strange results when adding a covariate in my 3dttest++ command.
Before adding it , results look as expected : ; but then with the covariate it looks like the field of view in being changed, (attached file) do you know what's happening ?
Thank you in advance
by
Lysianne
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AFNI Message Board
this command gives me: Intent_code offset: 68, nvals 1 and values 0
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Lysianne
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AFNI Message Board
the stats comes from APP, registered in Talairach space ,
then I use 3dAllineate to bring it back to native space, and keep only the t-stats from my contrast of interest in .nii format so I can use it with my neuronavigation software.
I was just being lazy and trying to find a way to extract the peak on my .nii file; I guess I can just switch the order of my steps and get the peak before c
by
Lysianne
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AFNI Message Board
but it says:
++ Looks like clustering is *not* being performed on a stat value; won't worry about sidedness, then.
** FATAL ERROR: Thresholding volume does *not* appear to be a stat so you can't use the 'p=..' internal conversion to stat
Even though my .nii is coming from a stat image
by
Lysianne
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AFNI Message Board
Hello you all,
I was wondering if there was an equivalent of 3dClusterize that would work for .nii files that do not have multiple sub bricks and therefore don't have an -idat and -ithr?
Thanks!
by
Lysianne
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AFNI Message Board
that would be great yes. So I can send you the result of this 3dNWarp as well
by
Lysianne
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AFNI Message Board
Unfortunately,
the lpa cost function does not really help. Results look pretty much the same
(disregard my former question - 3dAllineate allows to align to standard space without skull stripping)
by
Lysianne
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AFNI Message Board
running it now , will share results soon
Also another question, is there a way to use SSwarper only for warping - without skull stripping - I'm seeing the option to do skull stripping without warping with skipwarp; but is there a skipskullstripping ?
THanks
by
Lysianne
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AFNI Message Board
Hi Paul,
super sorry for the delay: I haven't seen your response earlier. Atthaching the anatS.nii here , there is a missing right parietal section and what I think is a some skin remaining in the occipital region
Will try to run with this extra command and see if it helps
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Lysianne
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AFNI Message Board
Hi I was wondering it there was any parameters I can play with on SSwarper cause I'm not super happy with the outcome (see attached file). it's cutting a bunch of the parietal area, which I'm interested in for the study.
Thanks in advance.
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Lysianne
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AFNI Message Board
Hello I would need to use a brain region from the DD_Desai_MPM atlas .
It's indicated on the website that is uses the TT_N27 template space
but I'm wondering what the difference between the TT_N27 and the TT_152_2009c
cause the 2009c looks way better for resolution and I would like to use that instead.
Any link I can find about that?
by
Lysianne
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AFNI Message Board
Hi you all,
I'm using 3dNetCorr to extract the times series (from task and from resting state) between 2 ROIs . I just found out that by adding -ts_wb_corr it also provides whole brain connectivity between each of those ROIs and the rest of the brain , which is super cool .
My question is: it returns this warning: "XX voxels skipped because were constant in time" . I read
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Lysianne
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AFNI Message Board
I think it actually finally worked!!
the only thing is that it;'s using TR = 3 while my TR = 2 (see below) is there any way I can edit that?
++ STAT automask has 46932 voxels (out of 411825 = 11.4%)
++ Skipping check for initial transients
++ Input polort=3; Longest run=405.0 s; Recommended minimum polort=3 ++ OK ++
++ -stim_times using TR=3 s for stimulus timing conversion
++ -st
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Lysianne
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AFNI Message Board
Hi I'm still struggling with this section, I'm getting an error specific to the 3dDeconvolve section (that I'm pasting below)
I created my txt files in the attached document (I just have one run and random timing - at the moment to debug my script )
This is the error I'm getting (I looked for this error on this board, one person has solved it by adding stim_times_AM1 but i
by
Lysianne
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AFNI Message Board
Oh gotcha , I was planning on using a GAM function since I used double gamma HRF in FSL and it seems to be the closest approach but I think I will use block(1) given your comment,
Thank you so much for the fast response.
by
Lysianne
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AFNI Message Board
Hi I'm starting to write a script to process fMRI data. I would like to use participant's reaction time as the duration of each event. I'm coming from FSL word where I would set up a 3-column text file with onset duration and weight and so would set up the duration as the RT. I can't find how to do the same with AFNI, could you help me figuring that out?
by
Lysianne
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AFNI Message Board
Hi you all,
I'm trying to use the 3dAFNI2NIFTI command to convert my stats map (after analyses) in NIFTI format to be ready by a neuronavigation software. However I'm struggling with it cause I think the default are exporting the Fstats from the full model. How can I modify this so that it will convert only my contrast of interest?
I tried adding "idat X" (with X bein
by
Lysianne
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AFNI Message Board
Hmm I see, but I guess the voxel size will be different since the EPI might have lower resolution than the T1, no?
Also this will be done only on a subject-to-subject basis, it's just for individualized targeting approaches.
Here is the command
3dAllineate -base ${anat} -input ${maskdir}/MNI152_2009_template.nii -prefix ${wdir}/MNIinNative_formatrix -1Dmatrix_save transformation_ma
by
Lysianne
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AFNI Message Board
Thank you for your answer,
I used 3dAllineate, first by moving the MNI space to native space in order to generate the transformation matrix and I then applied this matrix to convert the mask into native space
This is the output from 3dinfo -same_all_grid:
0 0 1 1 1 stats.test
0 0 1 1 1 WenickeinNative
That is the output from 3dinfo -space:
ORIG
by
Lysianne
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AFNI Message Board
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