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 - 17 of 17
Dear AFNI developers,
I'm reposting this question, could you help me out with this issue?
Thank you!
All the best,
Irene
by
irepe
-
AFNI Message Board
Dear AFNI developers,
I’m running 3dTfitter in preparation for a PPI analysis.
The output time series of 3dTfitter has large spikes at the beginning and at the end of the run (spikes.jpg).
The time series of the ROI seem ok to me (roi.jpg).
Below, I include the commands I used, together with the output.
Could you help me in identifying what the source of the spikes might be?
T
by
irepe
-
AFNI Message Board
Dear Paul,
It seems that using @Align_Centers with no deobliquing either at 3drefit or @SSwarper resulted in good skullstripping and alignment.
Attached are screenshots from the index.html files using the first setting vs the current one.
The first setting used (see A in attachments) :
@SSwarper -input ${T1_data} -base MNI152_2009_template_SSW.nii.gz -deoblique_refitly -subid ${sub_id}
by
irepe
-
AFNI Message Board
Hi Paul,
Thank you for your prompt help.
> Basically, my guess is that your dset starts out
> far from overlapping on the template dset; you
> can check this with:
>
> 3dcopy ${T1_data} test_copy.nii
> 3drefit -space TLRC test_copy.nii
>
Yes, the T1 and the template did not overlap (see A in the attachment).
> In your particular case, I think this h
by
irepe
-
AFNI Message Board
Dear AFNI experts,
I'm also having a similar issue. I've run the following script:
@SSwarper \
-input ${T1_data} \
-base MNI152_2009_template_SSW.nii.gz \
-deoblique_refitly \
-subid ${sub_id} \
-giant_move \
-odir $startdir/pre_warp_${sub_id}
A large portion of the anatomical image is missing after second pass skull-stripping (see attachments). Any ideas of what might b
by
irepe
-
AFNI Message Board
Thank you Gang,
I added the GLTs:
'Group : 1*control Category : 1*iaps Corr :' \
'Group : 1*patient Category : 1*iaps Corr :' \
For the controls I get basically all the clusters I had for the initial 3-way Group*iaps*Corr interaction. The t-scores are all negative for these clusters.
For the patients I dont get anything.
Can I conclude that the controls hav
by
irepe
-
AFNI Message Board
Dear Gang,
Thanks for your help.
> More accurately, GLT #4 looks for the difference
> of association between beta and 'Corr' between the
> two group when Category is fixed at 'iaps'.
Am I right in interepting association as correlation? If not could you please explain what you mean with association?
My main struggle is to find ways to make this 3-way int
by
irepe
-
AFNI Message Board
Thank you Gang,
I have two follow-up questions:
1) The output of glt4 from the initial 3dLME:
3dLME -prefix LME_results -jobs 1 \
-model "Group*Category*Corr" \
-qVars "Corr" \
-ranEff '~1' \
-SS_type 3 \
-num_glt 4 \
-gltLabel 1 'Group' -gltCode 1 'Group : 1*control -1*patient' \
-gltLabel 2 'iaps_vs_shape' -gltCo
by
irepe
-
AFNI Message Board
Thanks Gang!
> The model seems fine in general. Is 'Category' a within-subject variable?
Yes. In reality it has 4 levels.
> Do the groups differ substantially in "Corr"?
I compared the scores between groups for each level in the within-subject variable "Category". When doing that I find no significant difference between the groups, except for one
by
irepe
-
AFNI Message Board
Thanks Gang!
After changing to InputFile I got this error:
During startup - Warning message:
Setting LC_CTYPE failed, using "C"
Read 515 items
Error in `[.data.frame`(dataStr, , vars) : undefined columns selected
Calls: process.LME.opts ... gl_Constr -> glfConstr -> levels -> [ -> [.data.frame
Execution halted
Which was fixed by adding a space before each colo
by
irepe
-
AFNI Message Board
Dear AFNI experts,
I'm having some issues with my 3dLME command and would be grateful for some guidance. The design has:
1 between-subject factor "Group" with two levels: "control", "patient"
1 within-subject factor "Category" with two levels: "shape", "iaps"
1 within-subject covariate "Corr"
When I run file_too
by
irepe
-
AFNI Message Board
Hi Rick,
Ok, I understand, thanks for your explanation.
The collinaerity is high between the regressors related to the "q" and "c" events.
For the regressors during the "o" event there's a medium collinearity only with the motor regressor (see below).
Am I correct in assuming that the results for the "o" regressors are more solid and can
by
irepe
-
AFNI Message Board
Dear Rick,
Thanks for your help and explanation, it really helps.
-How many time points are there?
Each trial lasted 8, 9 or 10 seconds and was divided in 3 within-trial events: “q” (3 sec), “c” (2, 3 or 4 sec) , “o” (3 sec).
For event “q” we had two possibilities/regressors (“qs” or “qo”), same for regressor “c” and for event “o” we had 4 possibilities/regressors (“ood”, “oou”, “osd”
by
irepe
-
AFNI Message Board
Dear Rick,
Thanks for your email.
The trials lasted either 8, 9 or 10 seconds. More specifically, each regressor lasted the following:
-stim_times_AM1 13 ${stim}/.. 'dmBLOCK' -stim_label 13 'qo' \ ----> duration 3 seconds
-stim_times_AM1 14 ${stim}/.. 'dmBLOCK' -stim_label 14 'qs' \ ----> 3 seconds
-stim_times_AM1 15 ${stim}/.. 'dmBL
by
irepe
-
AFNI Message Board
Dear Gang,
Thanks for your prompt reply and help.
I did what you suggested. I'm attaching the graphs with fitts (black) and all_runs (my input data, in green) overlayed. Do you have any insights?
Thank you!
All the best,
Irene
by
irepe
-
AFNI Message Board
Dear AFNI experts,
I run two 3dDeconvolve commands, one using a GAMMA function and one using a TENT function (see commands below).
In order to inspect whether the output using the TENT function for a specific condition was consistent with the results computed using a GAMMA function, I’ve uploaded both the -iresp output (underlay) and the stats output (overlay). I'm assuming a coheren
by
irepe
-
AFNI Message Board