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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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Yes, the third info break down was from the dataset I posted images for and was from the Z -> R "undoing" atanh step.
And yes I used the [0] subbrik as per Mr. Chen's how-to: "And if you want the correlation coefficient at group level, you can convert the z-score (sub-brick #0 in the output from the group analysis) back to r (the reverse conversion of step 9 above):.
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d6anders
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AFNI Message Board
Ok, so not sure which dataset exactly you wanted info for. Will include major ones, sorry for so much info.
so this is for the bucket dataset I got from 3dDeconvolve using the motion regressors, the raw ROI timeseries, and the contrast Interaction term. I used the R^2 and Coeff ie. '[16] and [14] from this dataset to do the 3dcalc R->Z transform and atahn.
Template Space: TLRC
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d6anders
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AFNI Message Board
Isn't the mean subbrik caused by running a 1sample ttest to look at the group effect of the Interaction Term? I believe the label is simply carried over during the R-Z transform etc.. from Gang's CorrAna.html steps 7-8.
Should a different subbrik or something be utilized during the group analysis? I admittedly probably missed something in all the steps.
~`Dane
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d6anders
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AFNI Message Board
Thanks for help. With your response and some of the previous answered questions about errors on the community board I managed to make it through everything and have results.
I did however notice something weird. The lower I slide the threshold bar the stronger and larger my clusters become. Directly opposite of what happens in most analyses. Why with a lower P value do you see more effects? S
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d6anders
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AFNI Message Board
Hey guys,
Trying to properly understand beginning steps of Context Dependent Connectivity Analysis (ie. /gangc/CD-CorrAna.html and Cisler 2013 paper) before I tackle it actively. In both the above sources it says to use as an input file, the subject data "which you have already run regression analysis on with 3dDeconvolve". Next you create your interaction regressor by multiplying y
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d6anders
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AFNI Message Board
So given a full night "(Calculations finished; elapsed time=79339.229)" things completed, however a few warnings I was curious about came up
WARNING: Input dataset is not 3D+time; assuming TR=1.0 (TR's should be 2.5)
++ Output dataset ./sum_ideal.1D
and
**failed to init basics...
Either anything to worry about?
~`Dane
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d6anders
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AFNI Message Board
No please don't worry about it. I simply appended it into the proc.SUBJ file as such:
1dBport -nodata $nt 2.5 -band 0.008 0.07 -invert -nozero > rm.bpass.1D
1d_tool.py -infile rm.bpass.1D -pad_into_many_runs $run $#runs -set_run_lengths $tr_counts \
-write bpass.r$run.1D
The execution however is taking a long time on my practice subject. I am afraid it may b
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d6anders
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AFNI Message Board
That seemed to get things moving. I used a concatened version of the motions files + your edits and Afni_proc.py finally ran and generated a script. This would start to run but I ran into two problems:
1. Its chokes when compiling the badpass regressors because my runs are different lengths see error below. So I altered generated proc.SUBJ file to use cat rather then 1dcat. Seemed to work, b
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d6anders
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AFNI Message Board
Thanks. Was obvious once you pointed it out. Scripting is always an on going education(read here: pain *laugh*) for us psychology types. But the more I read and understand this python script the more glad I am to be learning it now for future work.
However, for the sake of time on this fast approaching project can you confirm there is no -argument such as -regress_bandpass built into 3dDe
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d6anders
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AFNI Message Board
Oh that's ok, glad you are back. I will speak with colleagues and check into the full model regression option. In the mean time I did my best to rework the python script with your suggestions. Unfortunately I am getting this error repeatedly. We have the updated python script in our abin so I am confused why this is occuring.
--regress_censor_extern: Command not found.
-regress_stim_fil
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d6anders
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AFNI Message Board
Hi Rick,
So the data is archival and unfortunatley a rapid event related design with randomly interspersed conditions (ie. no convenient blocking); obviously not ideal for FC. Therefore we did 3dDeconolve -errts independently for each condition. For condition A: regressing out B + C, for B: regressing out C + A etc and so forth. Then within each version of the data we cut out task events of
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d6anders
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AFNI Message Board
Thanks for rapid response rick. For "a bit unconventional" I was referring to my decision to both try and remove the lowest, hopefully intrinsic, frequencies, and doing so inside a task based functional connectivity analysis between task conditions. Working in a lab that focuses mostly on resting state FC this is all way out in left field. *laugh*
OK so, I am doing this all the old-s
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d6anders
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AFNI Message Board
Hey guys,
To begin with I know what I am trying to do is unconventional, but I still need to accomplish it to test a theory... so foregoing the whys, any help you can provide on the how would be much appreciated.
Basically I am trying to filter out the lower -intrinsic- frequencies from a task based data set, to then run an ROI-to-ROI functional connectivity analysis focused on task effects
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d6anders
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AFNI Message Board
Hey all,
We are creating a the Pearson's coefficient, correlation matrix created between time series from several ROI's. To do this we are using the 1ddot with the -dem option. The hope was you might be able to fill us in on how the program deals with missing data. And how to best represent those removed time points so they don't throw the results off.
For instance when leav
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d6anders
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AFNI Message Board
Hey guys,
I am trying to create a mask of "Area 6" (atlas label 210) of the TT_N27_CA_EZ_MPM atlas, and having some problems. Endeavored to use:
3dmaskave -mask TT_N27_CA_EZ_MPM:both:Area 6 Func+tlrc
but AFNI informs me it can't read the mask dataset. I assume this means I am not referring to the atlas and/or subarea correctly in the script but want to be sure. I pulled
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d6anders
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AFNI Message Board
Thank you rick. This looks perfect. Is there anyway to model the HDR just the specific TRs of these events (generated by the .py script) in 3dDeconvolve, or will everything have an extended hemodynamic tail like BLOCK?
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d6anders
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AFNI Message Board
Did anyone have any response on this?
I also wanted to include a similar question:
Is there a HDR modeling function in 3dDeconvolve or 3dDetrend where I can specify exactly which TR's will constitute the entire length of the model? ie. Getting the program to create a HDR function that begins at TR #3 and ENDs specifically on TR #9?
Thanks. I know this is hardly standard way to
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d6anders
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AFNI Message Board
I see your point. I supposed the issue is I am trying to utilize the program in a slightly different way.
Our hope was that 3dDeconvolve could be used to create a series of binary .1D files to assign appropriate TRs to each of our interspersed rapid Event Related design conditions (with the appropriate HDR lag). This would allow us to censor out certain conditions to properly parse the data fo
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d6anders
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AFNI Message Board
Thanks Rick. That was very helpful and cleared things up. I was hoping to follow up with a side question however.
We used dmBLOCK for the initial analysis due to varying lengths of the stimuli. As I go through the xmat.1D files I am noticing how LONG after the stimuli the functions continue. I thought the HDR is typically thought to have a lag of about 5-8 seconds. The 3dDeconvolve literatur
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d6anders
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AFNI Message Board
Apologies, forgot to add that the TRs are 2.5 seconds. So 1 or 2 TR's certainly do not cover the 15 seconds I am looking for.
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d6anders
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AFNI Message Board
Hey all,
I wanted to created some referrence files for when TR's are used for each of the conditions of my task... but when I looked at tent functions created via 3dDeconvolve (see script below) it only provides BOLD data at singular points rather then extended groups over the (3,18,7) I specified in the script. More over it has the same Bold values across what should be different TR'
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d6anders
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AFNI Message Board