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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,
If anyone has a good multi-band EPI protocol for a GE 750w 3T magnet, I would really appreciate it if you could share here or directly to me (jatin-vaidya@uiowa.edu).
Thanks,
Jatin
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jvaidya
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AFNI Message Board
I'll have to do some checking. The MacPro I ran on also has 32 GB of RAM. How long should one job take?
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jvaidya
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AFNI Message Board
Thanks for the suggestion. I tried @SSwarper and the processing did not fully finish. Seemed to get stuck on my iMac and got a broken pipe error on a MacPro. However, I think the final skullstrip image was created and that does indeed look much better (though some cleanup near midbrain could be added). How much memory and processor speed is necessary for @SSwarper? If this works well, I'
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jvaidya
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AFNI Message Board
Hi,
We are having trouble with getting the eye area removed. We have tried playing with shrink factor up to .9. While that helps clean up things near brain stem, we still have eyes present on many scans.
Do you have a some 3dSkullstrip parameters that might work for this sort of problem?
Thanks,
Jatin
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jvaidya
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AFNI Message Board
Hi,
I want to create a mask of all subjects and sessions in my study. I have 80 subjects who have resting state scans at two time points. Data have been preprocessed and warped into template space. I'd like to create a mask that includes voxels from all subjects and sessions. In other words, I'd like to mask out any voxels where there isn't data available for everyone at bo
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jvaidya
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AFNI Message Board
Hi,
I have T1 images from different scanners that I'm trying to convert to nifti format. I tried to3d with the -anat option but the results were clearly wrong. I am now trying Dimon but am getting an error. I'm in the directory that has the .dcm data and here is the command line:
Dimon -infile_pattern '*.dcm' -gert_create_dataset -gert_write_as_nifti
The error I ge
by
jvaidya
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AFNI Message Board
Hi Rick,
Here's the command I ran for one subject with one resting state scan (again, I'm preprocessing in AFNI but need to run group ICA in GIFT).
1d_tool.py -infile Rest_mt.1D -set_nruns 1 -derivative -collapse_cols euclidean_norm -write motion.txt
I think I may not be understanding what -collage_cols euclidean_norm is doing without the "-derivative" option. Here&
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jvaidya
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AFNI Message Board
Hi,
I am checking out the functionality of 1d_tool.py to create an overall framewise displacement score (euclidean_norm) for each subject to run group ICA analyses in GIFT (preprocessing done in AFNI). My understanding is that for each time, you take each of the rotation and displacement values and subtract from the one just before. This value is squared for each of 6 displacement/rotation c
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jvaidya
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AFNI Message Board
Sorry, here's a bit more information...
My understanding is that two time series may appear to have a weak correlation with one another but in fact could show similar associations if one took into consideration the time lag. For instance, one time series may simply have a phase that is pushed forward a bit more than the other (but not enough to result in negative correlation). Cross cor
by
jvaidya
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AFNI Message Board
Hi,
Is there a way to run a cross-correlation for resting state that incorporates lagged associations? I looked at 3dfim+ and it doesn't seem like it deals with lags.
Thanks,
Jatin
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jvaidya
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AFNI Message Board
Hi Rick,
Thank you for catching that! I have fixed this issue and am running into an error that I can't figure out. For some reason, during one of the anaticor related steps, there is a problem with 3dTcat.
3dTcat -prefix all_runs.131001_64415311 pb00.131001_64415311.r01.tcat+orig.HEAD
++ 3dTcat: AFNI version=AFNI_16.0.00 (Jan 1 2016) [64-bit]
3dTcat -prefix rm.all_runs.volreg
++
by
jvaidya
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AFNI Message Board
Hi All,
We're using afni_proc.py to conduct seed based resting state analyses. I'm trying to remove motion, signal from ventricles, and LOCAL white matter. However, based on the proc_script.sh file, it seems that the local white matter step happens at a separate point and therefore it does not seem like I have a final cleaned dataset that removes motion, signal from ventricle and s
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jvaidya
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AFNI Message Board
Hi All,
I think the de-oblique option did the trick in conjunction with the other suggestions. Here's what I did. The only issue now is that I think I need to add the -dxyz dd option to change the file to a lower resolution image as the file size is huge right now. Thanks for your help.
3dWarp -deoblique t1h.nii
3dcalc -prefix t1hd -a warped+orig -expr 'a'
rm warped+or
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jvaidya
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AFNI Message Board
James,
Thans, that did help quite a bit. The EPI is much closer to where it should be but still clearly not lined up. I did notice that there were some comments that I should consider deobliquing my T1 but I figured that is unlikely to be the issue if the EPI fits with the T1 after runnning align_epi_anat.py.
Would appreciate any additional thoughts.
Jatin
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jvaidya
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AFNI Message Board
Hi,
I've been trying for sometime to implement 3dQwarp and 3dNwarpApply. Qwarp seems to work great but I can't get my EPI image to line-up with the template. Here's an example script. I did check that the EPI got coregistered properly with align_epi_ant.py. I also checked that the t1 got registered to the TT_N27 template. I'm guessing that I'm doing something wron
by
jvaidya
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AFNI Message Board
Hi,
I have five runs in my experiment and I currently put all runs into one 3dDeconvolve model. However, I'm also interested in run effects. Is there a way to have 3dDeconvolve provide beta coefficients for each regressor/contrast for each of the five runs?
Thank you,
Jatin
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jvaidya
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AFNI Message Board
Hi,
I am using Go/No-go task and am wondering if it would be appropriate to have the amplitude modulation option for 3dDeconvolve. In the task, there are go trials (press button when you see any letter but the letter "x"). The no-go trials are the "x" trials. There many more go than no-go trials. I *believe* the amplitude modulation comes into play because the number go
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jvaidya
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AFNI Message Board
thanks daniel.
let's say there is no cut-off at all (i can collect a few more slices), is the coregistration going to be as good with the angled acquisition as the AC-PC? just to be clear, i've posted the AC-PC and -30 angle images here (same subject):
it might help if you look the axial slice to see the difference. the top row is the -30 angle.
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jvaidya
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AFNI Message Board
it has been previously recommended that a -30 angle (in reference to AC-PC) helps reduce signal artifact and signal loss i ventral prefrontal cortex and in other artifact prone regions like the amygdala.
i have collected some pilot data and it does appear that signal quality is better with the -30 angle.
i'm curious if there are any concerns with coregistration to a structural scan
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jvaidya
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AFNI Message Board