Show all posts by user
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
Page 1 of 1 Pages: 1
Results 1 - 14 of 14
Dear Afni experts,
I am not sure if I am selecting the correct sub bricks for visualization.
Usually, I select:
Olay: Condition 1 - Condition2:b
Thr: Condition1 - Condition2: t
However, I don't have this options now. The ones I have are:
Condition 1- Condition 2_mean
Condition 1- Condition 2_Zscr
Condition 1- Condition 2_covariate_L
Condition 1- Condition 2_covariate_L_Zscr
by
myriam.oliver
-
AFNI Message Board
HI!
I am trying to do a correlation analysis from a seed region, but the output does not make sense. I am following the steps in
The first error I am facing is in adwarp
$ 3dSynthesize -prefix effectsNoInterest -cbucket all_betas.bil+tlrc -matrix X.xmat.1D -select 0 1 2 4 5 6 7 8 9
++ 3dSynthesize: AFNI version=AFNI_17.0.09 (Feb 10 2017) [64-bit]
++ Authored by: RW Cox
++ Output has
by
myriam.oliver
-
AFNI Message Board
Great, Gang! My very last question..
Actually, double checking and correct me if I am wrong, the afni_proc.py provides the ACF values on the blur.errts.1D file, right?
Something like:
3.88582 4.19455 5.32402 4.42727 # epits FWHM blur estimates
0.831582 2.56576 7.90266 6.34748 # epits ACF blur estimates
3.84754 4.1605 5.35565 4.40941 # errts FWHM blur estimates
0.82605 2.54857 7.5910
by
myriam.oliver
-
AFNI Message Board
Hi Gang,
Do you mean I should not specify the residuals on the file. So instead of, 3dFWHMx -dset mema++.6_E-S_resZ+tlrc'[0:X:(2)]' -out E-S_FWHMx
Should be:
3dFWHMx -dset mema++.6_E-S_resZ+tlrc -acf -out E-S_FWHMx
thanks,
by
myriam.oliver
-
AFNI Message Board
Hi Chang,
What do you mean by 'estimate the ACF by using the residuals from the individual level'?
How should I do that?
Thanks
Myriam
by
myriam.oliver
-
AFNI Message Board
Thanks!!
So, I tried what you suggested plus adding the -acf command . But did not work (see below)
I have a total of 35 sub-bricks (see image attached)
3dFWHMx -dset mema++.6_E-S_resZ+tlrc'[0:34:(2)]' -acf -out E-S_FWHMx
++ 3dFWHMx: AFNI version=AFNI_17.0.09 (Feb 10 2017) [64-bit]
++ Authored by: The Bob
** ERROR: selector syntax error 5 ':(2)]'
** ERROR: bad sub-b
by
myriam.oliver
-
AFNI Message Board
Thank you Gang!
One more question,
-Just to double-check, I run 3dFWHM. are the acf values the ones written by: vary, vary and varzz? so, in the example below will be:
varxx=0.537552 varyy=0.504485 varzz=0.308338
3dFWHM -dset mema++.6_E-S_resZ+tlrc -out E-S_FWHM
user@dancer:./3dFWHM
++ 3dFWHM: AFNI version=AFNI_17.0.09 (Feb 10 2017) [64-bit]
++ Authored by: B. Douglas Ward
*+ WARNI
by
myriam.oliver
-
AFNI Message Board
Thanks Gang! It worked!
However, I don't understand the output. Now, I have three output files:
-mema+tlrc
-mema_ICC+tlrc
-mema_resZ+tlrc
The first one (mema+tlrc) is still the one uncorrected. But ICC & resZ shows sub-bricks of each participant individually.
How can get the comparison between groups (b & t values) but corrected by multiple comparisons?
Thanks!
by
myriam.oliver
-
AFNI Message Board
Thanks your answer, Gang!
However, when I run it with -residual_Z. The following error pop up
:** option -subs_tstats has illegal dashed parameter: -residual_Z
--> maybe parameter is a mis-typed option?
This is my script:
gen_group_command.py -command 3dMEMA \
-write_script cmd.mema.6 \
-prefix me
by
myriam.oliver
-
AFNI Message Board
Dear all,
I used 3dMEMA but I would like to correct the output.
Can I use ETAC? I am not sure if its only recommended for 3dttest++
If not, which other method should I use?
Many thanks!
Myriam
by
myriam.oliver
-
AFNI Message Board
Dear afni users,
I am trying to run afni_proc.py but I keep receiving the same error; Unmatched. Any help will be highly appreciated.
++ Output dataset ./mask_group+tlrc.BRIK
1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D
1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D
1d_tool.py -infile dfile_rall.1D -set_nruns 1 -s
by
myriam.oliver
-
AFNI Message Board
Dear afni users,
I am having a problem to run the 3dBlurToFWHM. The error is:
3dBlurToFWHM -FWHM 6 -automask -prefix rm.pb04.$subj.r$run.blur -input pb03.$subj.r$run.volreg+tlrc
++ 3dBlurToFWHM: AFNI version=AFNI_16.0.00 (Jan 1 2016) [64-bit]
** FATAL ERROR: Can't open dataset 'pb03..r.volreg+tlrc'
** Program compile date = Jan 1 2016
I tried the Is command, it seem
by
myriam.oliver
-
AFNI Message Board