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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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Pages: 12345
Results 1 - 30 of 147
Hi,
My paradigm is like this: R is 30 sec rest, T is 60 sec. task
R T R T R T
Total duration is: 270 sec. (tr: 2.5s total sub-bricks: 108)
I want to calculate PSC in 2 different methods:
1. Considering 1st rest block as the real rest and then consider the entire thing after that part of the task: (Iinput in STIM file is 30 and that's it. And we can get PSC by
by
pshuk
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AFNI Message Board
Hi,
I am also getting the same error. Even though they have same grid spacing and size.
here is my script.. Can anyone help..
#!/bin/tcsh
3dttest++ \
-prefix /mnt/Processing1/Priyank/ANALYSIS/MOUSE/Mouse.Wild-GAG.t++.Mouse_Striatum \
-setA Wild \
45_01 '/mnt/Processing1/Priyank/MOUSE_out/s_20150206_Li_mouse_45_01/Z_pearson_s_20150206_Li_mouse_45_01.Mouse_Striat
by
pshuk
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AFNI Message Board
Hi,
I am doing this mouse study in which having 2 problems.
1. It is reading Axial as Coronal and vice versa. FOV is also different along these two directions. I tried
2. voxel size information from AFNI is not right.
FOV is 19.2 x 19.2 x 0.75 mm
No. of voxels: 256x256x12
voxel size from AFNI: 0.192x0.192x0.75
but it should be 0.075 x 0.075 x 0.0625
I tried 3drotate -rotate
by
pshuk
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AFNI Message Board
thanks. That is a good suggestion. We also came to the conclusion to use one random mouse's anatomical as the template. Moreover, we are not collecting whole brain so this approach makes much more sense rather than relying on some Atlas.
Thanks
by
pshuk
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AFNI Message Board
Hi Afni Gurus,
I have to analyze mouse resting state data. And I was thinking of using my resting state pipeline (tested on human data) for mouse with some tweaks. But I have some concerns:
1. I know, I can't use MNI template, do we have option to use mouse brain template in AFNI and how do we edit that in proc.py?
-base Mouse_Atlas ??
2. Resting state and T1
by
pshuk
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AFNI Message Board
yes as gang mentioned, TR = 2.5s. No I want to get response after removing the rest period. So I created new EPI with only the TRs that correspond to task and remove all the rest periods from the file.
I will try 3dDetrend and see how it helps.
I added resting period at the end and it ran fine. Let's see what it does.
Thanks for your help ..
by
pshuk
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AFNI Message Board
Thanks Gang,
One quick question also. How do I get interaction between grp and task ?
I have one line for that but that is only for 2 groups, how to include all 3 ?
by
pshuk
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AFNI Message Board
Hi,
I want to try a new method to analyze my data. Here is my paradigm:
Rest period...Task...Rest...Task...
Task period is 30s. I want to analyze with rest period out of my EPI.
So, I created another EPI using TRs when subject is performing task only.
Total task time=240s
I added first rest period of 30s in the EPI also.
Now, I am trying to run TENT(-10,240,101) but it is giving
by
pshuk
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AFNI Message Board
Thanks Gang,
That fixed it but I am getting this error now.
Error in gltRes[] : subscript out of bounds
by
pshuk
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AFNI Message Board
Hi,
I am trying to run ANOVA with covariate, so using 3dMVM.
I have 3 groups and 2 conditions and Age and Gender are used as a covariate.
I want to get the effect of covariates alone and combined . Here is a sample script, I wrote which is giving me this error on execution:
Incorrect level coding in variable Group :F
Incorrect level coding in variable Group :M
here is my script:
by
pshuk
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AFNI Message Board
ANOVA3 - 9 years ago
I want to design my analysis
alevels 3 Groups
blevel 2 time points (baseline and a year after)
clevel 2 tasks
So I design ANOVA3 with type 1 (everything fixed)
Now how do I get aBdiffs because it is giving me the error message.
by
pshuk
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AFNI Message Board
Hi,
I am running 2 analyses:
1. we fit the BOLD signal to BLOCK(30,1) function
2. analyzing connectivity between different brain regions while they are performing task.
What I understood so far, you apply SFNR to BOLD signal (1st method). Am I right?
Can the same method be applied to 2nd analyses too? I use errts.anaticor file to get correlation maps for brain regions. Can I apply 3dT
by
pshuk
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AFNI Message Board
I am sorry but just to be sure that I got it right.
1. I run AFNI_proc.py as usual for my BLOCK function and get the final results (stats file, along with other pb files)
2. Take pb04 (last pb file) and apply 3dTstat -cvar to get SFNR voxel vise
3. Use that file for each subject as a covariate in t-test.
Is this right?
Now second option: regress SFNR in the file while running the proc.py
by
pshuk
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AFNI Message Board
Thanks Peter
I want to take the SFNR within an "unrelated" ROI and regress that out of your other ROIs. How can I do it in Afni. Better if I can do it in proc.py.
by
pshuk
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AFNI Message Board
Thanks Peter,
So I apply that to the final stats file that I get from Afni and it will give me SFNR file. Do I still have to detrend my files, like add detrend option in my proc.py along with block tshift regress align mask scale options? I just want to be sure that I am doing it right.
Your help is much appreciated.
Thanks
by
pshuk
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AFNI Message Board
Hi,
I am doing a study right now for which half of the subjects are scanned at place1 and other half at place2. fMRI machines are different. I simply performed ANOVA and checked the between site effect and it seems significant. Anyone has suggestion about how to perform multi-site analysis, kindly share.
Thanks
by
pshuk
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AFNI Message Board
Hi,
I want to find maximum value in one of the sub-bricks of my file but at the same time, I want to have an upper limit on it. Is there a simple way to do this?
I know 3dBrickStat will give me the max but I am not sure how to set an upper limit.
I thought of creating first a mask by: 3dcalc -a file -expr 'isnegative(a-limit)' -prefix mask
apply the mask to original file: 3
by
pshuk
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AFNI Message Board
they are 3 mm sphere.
Strange thing is: 2 ROIs are exactly same in shape and size, only location is slightly different (still close to each other) but one resamples fine while other doesn't.
master file has 3x3x3 grid space and these ROIs are in 2x2x2.
by
pshuk
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AFNI Message Board
Hi,
I am resampling ROIs using 3dresample -master option but a couple of them producing nothing. What could be the reason.
here is the command I am using:
3dresample -master errts.same_anaticor.12066+tlrc -prefix res_Left_VP4_sph3_same -inset Left_VP4_sph3+tlrc
resampling of VP4 is fine but VP5 is not.
Even with -rmode NN option, it is giving same output.
by
pshuk
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AFNI Message Board
Hi Rick,
I also want to include RSFC to calculate ALFF, fALFF. I have my proc.py set up like this. But as I went through the posts here, I think I need to remove bandpass and regress_ROI option from my script. Please let me know, what do you think:
-------------------------
afni_proc.py -subj_id $sub -script $scrpt_file \
by
pshuk
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AFNI Message Board
Hi,
I want to use 3dvolreg -base last -heptic -clipit -zpad 4 in my afni_proc.py script.
I tried this: -volreg_align_to last \
-volreg_interp -heptic -clipit \
-volreg_zpad 4
but it is not recognizing the clipit option and giving error. Can someone please le
by
pshuk
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AFNI Message Board
yea, it's not Nifti files. As I converted files to AFNI format and still getting the same issue.
Afni version is : linux_openmp_64: Jul 1 2014
afni_proc.py -subj_id $sub \
-script $scrpt_file -scr_overwrite -out_dir $out_dir \
-blocks tshift align tlrc volreg b
by
pshuk
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AFNI Message Board
I am also getting this error. I tried updating AFNI but it didn't work.
Is it because I am using NIFTI files (.nii) instead of AFNI (+orig.HEAD) ?
Thanks
by
pshuk
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AFNI Message Board
thanks Rick.
I gather they should have separate processing to be on safer side.
by
pshuk
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AFNI Message Board
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Pages: 12345