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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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Hi discoraj,
1) There was an error when I ran ClustExp_StatParse.py. And I don't know what the outputs mean:
...
Resampling master to subject data.
-- will fix any bad char check errors in /media/data/MyOutput_CleanSubjTab.1D
** non-Unix check output file '/media/data/MyOutput_CleanSubjTab.1D' exists, will overwrite
-- will fix any non-Unix check errors in /media/data/MyOu
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Ren Po
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AFNI Message Board
Hi Rick,
Thank you very much for your helpful answers! I've got four more questions about the PPI demo in AFNI_data6:
1.How to do group analysis if there are many subjects ?
I ran the PPI demo following the instruction of README.txt and the results file PPI.full.stats.FT+tlrc was generated. See the brick labels in this dataset:
I don't know how to do group analysis and I thi
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Ren Po
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AFNI Message Board
Hi,
I am very sorry to trouble you again. The demo in the learning materials (PPI) you mentioned is also about block design fMRI with the duration of 20s. I have read every word in the learning materials you provided but I haven't found the answers. On the contrary, they make me more confused because some operation in these materials is so different from the link I mentioned(gPPI). The que
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Ren Po
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AFNI Message Board
Hi AFNI experts,
I will do gPPI analysis to my fMRI data with event-related design. I read the tutorial of gPPI (https://afni.nimh.nih.gov/CD-CorrAna) and I have some questions :
1) How to select a impulse response function in step 3?
A impulse response function is assumed firstly. And then the seed time series is deconvolve (step 3) and Inter_neuA.1D is convolved (step 4) using this re
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Ren Po
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AFNI Message Board
Hi Rick,
I just edited my last reply to make the meaning clearly. So you mean that the matrix in 3d_anat+card_al_junk_mat.aff12.1D is the forward transforming matrix from EPI to the file called something with _junk rather than 3d_anat+card+orig? The anat->EPI dataset is considered junk. So the skull-stripped version anat 3d_anat+card_ns+orig is not aligned with EPI (the first functional vo
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Ren Po
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AFNI Message Board
Hi Rick,
I am sorry for the careless comment given by myself in the align_epi_anat.py step firstly. What I really want to mean is that the aim of this step is to align the original anat (3d_anat+card+orig) to the EPI. And the aligned result is saved in dataset 3d_anat+card_ns+orig and the forward transforming matrix from EPI to 3d_anat+card+orig was written to file 3d_anat+card_al_junk_mat.aff
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Ren Po
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AFNI Message Board
Hi,
I found the EPI and Anat were aligned to different bases in the code generated by defaut proc.py:
#The Anat dateset 3d_anat+card+orig was aligned to the first volume of the first run.
#And the forward transforming matrix from EPI to 3d_anat+card+orig was written to file
#3d_anat+card_al_junk_mat.aff12.1D.
align_epi_anat.py -anat2epi -anat 3d_anat+card+orig \
-save_skullstr
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Ren Po
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AFNI Message Board
Hi Rick,
I compare the data of one subject as representative.I can see only tiny difference at the outer contour of the brain on final_anat+tlrc between the two methods.And the ROI seems to overlay both the old and new anat dataset well.But I am worried about some key difference can't be seen by the naked eyes.And the key difference can't be seen can cause bad overlaying between the
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Ren Po
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AFNI Message Board
Hi Rick,
The ROIs were drawn on the old dataset '*_ns+tlrc' in tlrc space which seemed to have been aligned to the EPI in the steps of align or volreg in previous analysis using uber_subject.py. I think these ROIs couldn't match the new anat datasets '*_ns+tlrc' or EPIs any more. Because the new anat datasets '*_ns+tlrc' were aligned to the EPIs with new anal
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Ren Po
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AFNI Message Board
Hi,
My anat (1mmX1mmX1mm each voxel) and EPI datasets (1.5mmX1.5mmX1.5mm) were preprocessed using uber_subject.py before with the steps of auto block,despike,align,tlrc,volreg,blur,mask,scale and regress.Then ROIs were drawn on the basis of anat datasets.And I had spent too much time on drawing these ROIs.
Now a few days after that, the data is analyzed using a new pipeline: auto block,tsh
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Ren Po
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AFNI Message Board
Hi,
My analysis script was generated by uber_subject.py. And the EPI dataset had been already aligned to TT_N27+tlrc before did 3dDeconvolve in this script. But every time I open the dataset 'stats.sub01+tlrc' as an overlay using GUI . An warning message pop up: "Forced switch from 'Original View' to 'Talairach View' Click in Text to pop down."
D
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Ren Po
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AFNI Message Board
Hi Daniel,
1.Is the 'Where am i?' window more accurate because we always draw ROIs manually in that image window?
What's the transformation method of GUI?
How can I transformed the coordinates like the 'Where am i?' window do?
The results of all the coding method I had tried were different from the results given by 'Where am i?' window.If I just want to s
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Ren Po
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AFNI Message Board
Hi Gang,
Thank you very much for your answers!
1)Set aside the feedback of error mentioned above temporarily, do you think there are logical or usage mistakes in my scrip which was pieced together by rewriting the demo of one within-subject factor and one between-subject factor ?
2)When using 3dANOVA3 to do a two-way within-subject (or repeated-measures) ANOVA, do we need sphericity te
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Ren Po
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AFNI Message Board
Hi all,
I need to do linear mixed-effects (LME) modeling analysis of two within-subject factors in AFNI.
Factor1 has two levels: level1OfFactor1, level2OfFactor1.
And Factor2 has three levels : level1OfFactor2,level2OfFactor2, level3OfFactor2.
There are no demos of two within-subject factors in the help files.So I wrote my analysis script by rewriting the demo of one within-subject fac
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Ren Po
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AFNI Message Board