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Dear AFNI users-
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Sincerely,
AFNI HQ
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Hi Rick,
I am sorry for the late reply my attention had to move away from this issue. I am using a Linux machine and I ran afni_system_check.py -check_all. I certainly have python on my machine. Below are excerpts from the output.
which python : /usr/bin/python
python version : 2.7.5
instances of various programs found in PATH:
afni : 1 (/usr/local/afni/bin
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AFNI Message Board
I don't think that is the case I can talk to our system administrator but first I will try to run these subjects again. The strangest thing is that things ran fine for some subjects and not others. I don't know how the python path could temporarily disappeared.
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AFNI Message Board
During preprocessing AFNI crashes (seems like it can't find the python directory) but this error only occurs for a handful of our subjects. What might be the source of the problem and why is it not a consistent issue? Any input would be great appreciated.
3dbucket -prefix vr_base pb02.s8.r01.tshift+orig[2]
++ 3dbucket: AFNI version=AFNI_18.2.19 (Sep 27 2018) [64-bit]
align_epi_anat.
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Well even in the other container it can't find the base for some reason but I am simply inputing a path to a place were I have the templates (not a real solution but it works).
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Ah It must have been some sort of issue when I loaded it (not sure if that is the proper term). I have the same container in another location and it contains a ./Templates folder with the templates but this is not the case in the other container file.
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I just started using this afni container and my preprocessing pipeline seemed to be working just fine until I reached auto_warp.py. I get an error where it claims that it can't find the base. I attempted to run auto_warp.py with a few other bases but I am getting the same error. What might be behind this difficulty in finding the base images? Note: I am fairly new to the container world
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Thanks for your response and I am sorry for my late reply.
I see what you are saying. The end of the 10th second marks the start of the 6th TR assuming a TR of 2 seconds. My stimuli are TR locked with a TR of 1.1 seconds. I want a box car with a duration of 104.5 seconds (95 TRs) and based on your description instead of going with 'EXPR(0,104.5)1' I should go with 'EXPR(0,1
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AFNI Message Board
I am working with a mixed block event related design and I am looking for a way to make my block/sustained predictor a boxcar without delay. The model contains cue predictors so I don’t plan on having a ramp up (delay) for the boxcar. Currently I am using block as my basis function for the sustained predictor. If I am not mistaken block is a convolution of a gamma function and a boxcar functio
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AFNI Message Board
Based on an ancient post
It seems that one can conduct another glt without re-running everything you had in 3dDeconvolve. It seems that this can be done only when certain options were specified. The 3dDeconvolve documentation seems to indicate that -cbucket cprefix needs to be specified in order to run 3dDeconvolve with xrestore. Is it possible to run a glt without having specified -cb
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AFNI Message Board
Interesting update if I take voa out of the model things look normal
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3dDeconvolve.err gives me the stuff posted below (I am aware two events are outside the range of the scan (scans got cut short).
*+ WARNING: Input polort=3; Longest run=484.0 s; Recommended minimum polort=4
*+ WARNING: '-stim_times 6' (LOCAL) run#1 has 1 times outside range 0 .. 438.9
*+ WARNING: '-stim_times 11' (LOCAL) run#1 has 1 times outside range 0 .. 438.9
*
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Update: I gave it a try yesterday and it does not solve the problem (still getting extreme values).
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I checked 3dDeconvolve.err and there was no multicollinearity warnings.
I posted the stuff below before but this is found in the recorded output
Warnings regarding Correlation Matrix: X.xmat.1D
severity correlation cosine regressor pair
-------- ----------- ------ ----------------------------------------
medium: 0.439 0.447 (122 vs. 297) corr6#17 vs. vo
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AFNI Message Board
Could PSFB syndrome cause the strange betas? Two events were cut off due to scans terminating prematurely. I can remove them from the event files but I am not sure how this would lead to the abnormal betas.
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AFNI Message Board
Yes the TR is 1.1 and when checking the timing files it seemed that all the values were divisible by 1.1 (hopefully I did not miss a simple erroneous onset value, I am checking again). The last time I used TENT I had to use the timing tool due to a TR locking issue but in that situation there was an extreme beta value at the first point (you mentioned how it is strange to have extreme values for
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AFNI Message Board
Here it is
within-TR stimulus offset statistics (corr1_3.txt) :
per run
------------------------------
offset means 0.880 1.100 1.100 1.100 1.100 1.100
offset stdevs 0.492 0.000 0.000 0.000 0.000 0.000
overall: mean = 1.035 maxoff = 1.100 stdev = 0.2668
fractional: mea
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AFNI Message Board
Okay just found this in the output
Warnings regarding Correlation Matrix: X.xmat.1D
severity correlation cosine regressor pair
but the correlations were all in the severity medium range (all in the .4s).
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Note: Had to change the TR value to reflect my scans
First off thanks again for your assistance. I ran timing_tool.py with warn_tr_stats and nothing showed up in the terminal so I assume it had no warnings. Next I ran timing_tool.py with the show_tr_stats option and the output was interesting. The mean offset was equal to my TR (stdev 0) for all of my stim conditions for all runs except th
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AFNI Message Board
I am running a model with 11 predictors (large number of tents for each predictor) and for all of the predictors I get this strange pattern. After the 14th TENT the betas have abnormal values. It should be noted that for one predictor the pattern is reverse things start off strange and the values enter the normal range post 14.
Any input regarding what might be behind this would be helpful
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AFNI Message Board
Thanks a lot for your input.
I think that there might be a hole in my knowledge about view vs. space.
The output below is from @auto_tlrc which was first applied to the structural and then I input the stats file into @auto_tlrc with the output of the previous step (transformed structural) being specified under option -apar.
*+ WARNING: Changing the space of an ORIG view dataset may
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I have two questions
When using a custom template you can simply specify the custom template as the base in auto_warp.py? Am I missing something regarding custom templates?
Also, I have been analyzing a single subject in the subject's native space and now I want to warp this subject to the template space. Is it unproblematic to warp the stats file to the template space? Right now
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The default for my terminal is bash. I plugged it into echo and I don't notice the \ characters.
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Interesting the thing is it is happening to all 14 of the contrasts and I am not seeing \ that are not at the end of a line. Maybe something is up with the text editor I am using (not what I typically work with). I wrote out the command in the text editor and pasted it into the terminal.
Here is an example of what is in the stats file for one of the contrasts (note this is true of all of
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Here is an update. I simply rewrote the the code I was having trouble with and it worked. Yesterday I attempted to do the same thing with another task but when using num_glt I got multiple coeffs and tstats for each contrasts. I removed some contrasts and reran without num_glt and now for each contrast I have two coeffs and two tstats. What might be causing this issue?
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I posted a short version I will send the actual version via pm. I just tried it again without spaces in the labels and it still crashes. 3dDeconvolve dies: Unrecognized command line option:
Thanks
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Note: It just occurred to me that for the glt labels I had two word names for many of them (with a space between them no _ like I usually use). Could this be the source of the problem?
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I have used gltsym before for contrasts but for reasons I don't understand (I thought it was a white space error or something) when it plug it into the afni proc the gltsym in the tcsh is all over the place for example ' separating parts of my titles. I ended up fixing the gltsym part of 3dDeconvolve on my own but I get command not found errors for gltsym. Below is an example of what
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AFNI Message Board
Okay! Now it makes sense the last answer totally confused me (I was expecting what you wrote in this message) and that is why I asked the follow up question. I should be more clear the average is my objective.
Thanks Again
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Okay thanks again Gang but there is still something I am missing here. What if I wanted to get the general effect across three instead of two conditions (P1, P2, P3) against baseline?
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