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 - 15 of 15
Hi Rick,
Thanks for your suggestion, which is great!
Because I have 1 run for resting and 5 runs for task fMRI, I decided to generate another sub-folder for each run, and to save the outputs in those folders, in order to avoid overwriting. For this I am doing something like:
for ((i=1;i<133;i++)); do
mkdir 5.1st_level_analysis/sub-${i}
mkdir 5.1st_level_analysis/sub-${i}/func
m
by
ruben.nechifor
-
AFNI Message Board
Hi,
This is the command I use (of course, with 2 loops for going through all the subjects - 1st loop - and all the runs - 2nd loop):
_________________
for ((i=1;i<10;i++)); do
for ((j=1; j<6; j++)); do
3dBlurToFWHM -input ${global_path}2.derivatives/sub-0${i}/func/sub-0${i}_task-stress_run-${j}_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz \
-prefix ${global_path}5.1st_l
by
ruben.nechifor
-
AFNI Message Board
Dear PT,
Thank you very much for your detailed and useful explanation! It is indeed important, needed and interesting to know those things!
However, I do not necessary and intentionally run the 3dFWHMx command, therefore I am not actually able to specify any of the options you present, so I am not able to have the output of the -ACF option saved separately (e.g. for each run a different fil
by
ruben.nechifor
-
AFNI Message Board
Dear AFNI experts,
I get the same error when I run the 3dBlurToFWHM command on my fMRI data, because after the blurring is done, the 3dFWHMx command is run check the results. In this case, since I am not running the 3dFWHMx command, how could I specify a different name for different fMRI data (e.g. different run), in order to have the output of the 3dFWHMx command in a different file (not over
by
ruben.nechifor
-
AFNI Message Board
Hi Gang,
I understand slope effect and intercept are two different outputs. In this case it will be fair enough to use the same parametric modulation for the all regressors included in contrasts (e.g. I and B), if we are sill interested in looking at some contrast (e.g. S-I, S-B)? Alternatively, we can use the parametric modulation only for a specific regressor, without considering any contras
by
ruben.nechifor
-
AFNI Message Board
Hi Gang,
For SPMG1, if the parametric modulation is related only to the regressor S, and I still want to see the contrast S-I, while for S is considered the parametric modulation effect, S[1]-I[0] shouldn't be an option? Taking a closer look at the experimental design, I am not convinced that the modulation effect can be attributed to the regressor I, so probably it will not make sense to
by
ruben.nechifor
-
AFNI Message Board
Hi Gang,
You are right, now for SPMG1 I have only one regression coefficient for I and B and two for S (and for SPMG2 I have only two regression coefficient for I and B and four for S).
So in this case, if I still want to see the contrast between the S regressor and I/B regressors considering the parametric modulation effect, what will be an appropriate approach?
1. for SPMG1: I should
by
ruben.nechifor
-
AFNI Message Board
Thanks Gang for your answers!
I have two other concerns:
A) Since the average of the two effects for SPMG1 (with and without parametric modulation) is not meaningful/interpretable, I wanted to obtain the individual contrast for:
1. the intercept, by doing this:
-gltsym 'SYM: S[0] -I[0]' \
2. and the slope, by doint this:
-gltsym 'SYM: S[1] -I[1]' \
However, wh
by
ruben.nechifor
-
AFNI Message Board
Thanks Gang for your quick and clear answer! It really helps me a lot!
I have few other questions please:
1. Now is clear to me that for SPMG1: S#0 will give me the intercept (and is associated with the major component of the hemodynamic response, as the first component from SPMG2, right? ) and S#1 will give me the slope, or the signal modulated by the parametric modulation of the function
by
ruben.nechifor
-
AFNI Message Board
Dear AFNI Experts,
I have some questions related with the order of the sub-briks saved when in the 3dDeconvolve we use SPMG1 and SPMG2 functions with parametric/amplitude modulation. More specifically, within my 3dDeconvolve I have a regressor (S=scenario) for which I apply one parametric modulator when the SPMG1 and SPMG2 functions is used. My questions are:
1. When the SPMG1 function is u
by
ruben.nechifor
-
AFNI Message Board
Dear AFNI experts/users,
I just want to confirm that this solution works for me too, on macOS Big Sur version 11.3 (MacBook Pro - 2020). Thanks for your help!
by
ruben.nechifor
-
AFNI Message Board
Thank you for your answer.
I did solve the problem by running the analysis on macOS Big Sur 11.3 (where this installation suggestion was very helpful, thanks for it!).
Do you think it worth to prepare and send you those data for further investigation? I did encounter this problem before, and at that time the solution was to remove one run for that subject (since I had 5 runs for each subject
by
ruben.nechifor
-
AFNI Message Board
Dear AFNI experts,
I try to run 3dDeconvolve with TWOGAMpw function for my subjects. For 5 out of 75 it is not working. I was looking on Message Board for help, and I found similar error, but for different function here . Over there the problem was related with affine alignment, so the solution does not apply to me. Could you please help me fix this? The error is:
3dREMLfit -matrix X.xma
by
ruben.nechifor
-
AFNI Message Board
Hi Gang,
Thanks for your reply.
I'd have another question: if I go for the omnibus approach, can I use the coefficients in a two factor two levels ANOVA, such that I'd have the two groups as factors and the two HRFs (amplitude and derivative) as levels, then look for a main effect of group?
I understand that the omnibus approach gives the coefficients for each function but I&
by
ruben.nechifor
-
AFNI Message Board
Dear all,
I run 3dDeconvolve with SPMG2 basis function and my GLT outputs are a bit unclear. If I specify the basis function with GLT (e.g. -gltsym 'SYM: S[0]' and -gltsym 'SYM: S[1]' ), then I get the results the same as the ones output automatically by 3dDeconvolve (S[0] for the gamma function and S[1] for the derivative). However if I do not specify the basis function in
by
ruben.nechifor
-
AFNI Message Board