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
Thank you, Gang, for your suggestion (that solution worked) and for the clarification of my questions.
Best regards,
Ekarin
by
Ekarin Pongpipat
-
AFNI Message Board
Oh, sorry, Gang, I should've explained the analysis a bit more.
This is a longitudinal analysis where the variables are:
1. con_linear (continuous-within) - a contrast of our within-subject functional task. Easy, medium, and hard conditions for each subject were coded as -1, 0, and 1.
2. age_w1 (continuous-between) - their age at wave 1
3. lag_years (continuous-between) - the differen
by
Ekarin Pongpipat
-
AFNI Message Board
HI AFNI Experts,
We were trying to create GLT codes for interactions of continuous variables, and we keep getting the generic 3dLME error (I'm assuming we're specifying our GLT for continuous variable interactions incorrectly).
For example, the following code without the interactions works (script 1):
3dLME \
-prefix $out_file \
-jobs 4 \
-model "con_linear*age_w1*lag_yea
by
Ekarin Pongpipat
-
AFNI Message Board
Hi AFNI experts,
I wanted to compare the results of using different contrasts for the psychological variable and also ensure that my understanding of the PPI term interpretation is correct.
The current recommendation is to use contrasts of 0 and 1 for the psychological variable, which allows the interpretation of the PPI term to be a change in the relationship between the seed region and ta
by
Ekarin Pongpipat
-
AFNI Message Board
I had a follow-up question on the IRF basis. If I was interested in comparing the results of not centering, mean centering, and zero-centering the PHYS term, how could I convolve the mean- and zero-centering PHYS term with one of the IRF bases and take that into account in the subject level analysis?
Thank you,
Ekarin
by
Ekarin Pongpipat
-
AFNI Message Board
Hi AFNI gurus,
I was just wondering if there was a method of choosing the radius of an ROI sphere? I can't seem to find a methods paper that addresses this? Would one typically use the lowest EPI spatial resolution or FWHM size? Or some factor of the former (e.g., double the lowest or double the FWHM)?
Thanks!,
Ekarin
by
Ekarin Pongpipat
-
AFNI Message Board
Thanks, Rick, I was planning on using the same basis function for the main regression. I was interested in comparing the differences in results using different basis functions (i.e., GAM, BLOCK, and SPMG1).
by
Ekarin Pongpipat
-
AFNI Message Board
If I wanted to use SPMG1 as the IRF, what should the ideal duration be?
Thanks!,
Ekarin
by
Ekarin Pongpipat
-
AFNI Message Board
Hi AFNI experts,
I had few questions about the script and generating IRF.
set dur = 15 # use a 15-second curve for BLOCK
set nt_irf = `ccalc -i "$dur/$TRup"`
set hrf_file = x.BLOCK.1D
3dDeconvolve -nodata $nt_irf 0.1 -polort -1 \
-num_stimts 1 \
-stim_times 1 1D:0 "BLOCK(0.1,1)" \
by
Ekarin Pongpipat
-
AFNI Message Board
Sorry, I did mean upsampling the seed time series. The TR is 1.5s and number of time points/volumes is 260; however, the stimuli onsets and durations occur outside of the TR. For example, the stimuli onset times are 5, 60, 115, 145, 200, 255, 285, and 340 seconds (total of 390 sec); and the stimulus durations are 25 seconds for the stimulus that occurs at 115 and 255 seconds and the duration is 5
by
Ekarin Pongpipat
-
AFNI Message Board
Hi AFNI team,
I had a similar problem. The functional scans were collected on a TR of 1.5. However, the stimulus times were not in TR times (e.g., 3, 155). I wanted to upsample the functional data to 1.5 so that the functional scans are in seconds. However, 1dupsample only allows for integers between 2 and 32. Is there another way to do this or an equivalent workaround? Your help is greatly ap
by
Ekarin Pongpipat
-
AFNI Message Board
Thanks, Rick, I installed fink, and uber_subject.py works now. Thanks!
by
Ekarin Pongpipat
-
AFNI Message Board
I have a similar problem and wasn't able to access uber_subject.py with a similar error message. After reading the message board, I also tried adding /sw/bin in front of the PYTHONPATH; however, to no avail. Specifically, within my .cshrc, the command is "setenv PYTHONPATH /sw/bin/usr/local/lib/python2.7/site-packages". Below is the output from running the afni system check. Any he
by
Ekarin Pongpipat
-
AFNI Message Board