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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
Page 3 of 5
Pages: 12345
Results 61 - 90 of 143
Hi,
Sorry for the delay...
What operating system and afni version are you using?
The @afni_R_package_install looks for the afni binaries folder and the "shiny" subdirectory in there to run OmicCircos_pkg_install.R for the -circos option.
It seems like your main afni GUI program is in /usr/bin/ but the other afni files are elsewhere.
I can modify the shiny programs to look elsewh
by
discoraj
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AFNI Message Board
Hi,
For the circos, there is not yet an option for the color bar.
I can try to add that.
Also for the circos, you can adjust the font size indirectly by changing the image size:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/FATCAT_matplot/FATCAT_matplot.html#id19
For the both the circos and heatmap png, I can add an option for changing the font size.
It will take a bit of tria
by
discoraj
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AFNI Message Board
Hi,
Give the 3dMVM_validator beta a try to test your -dataTable.
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/3dMVM_validator/3dMVM_validator_overview.html
It won't be correct for the 3dLME testing, but it should give you a hint for what is wrong with your -dataTable specification.
It is probably the quotes or some spaces somewhere.
Can you post some of your -dataTable?
by
discoraj
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AFNI Message Board
@FATCAT_matplot_shiny has been renamed to FATCAT_matplot for more shortiness.
by
discoraj
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AFNI Message Board
Hi,
I have shortened @FATCAT_matplot_shiny to just FATCAT_matplot.
I hope this does not cause too many problems. The previous name was just too painful.
Thanks, Justin
by
discoraj
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AFNI Message Board
Hi,
We updated dicom_hinfo to output the full entry (with spaces).
After updating afni, just add -full_entry like this:
dicom_hinfo -full_entry -tag 0008,0081 00001.dcm
Let me know if you run into any issues with it.
Thanks, Justin
by
discoraj
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AFNI Message Board
Hi,
I am working on a little script to do this for you.
Currently it can be done with ClustExp_StatParse.py, but it was designed to do much more.
And you will have to provide all of the other required inputs for it to output a mask.
It will output a mask, thresholded at a specified p value.
See here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/ClusterExplorer/Introduction.
by
discoraj
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AFNI Message Board
Hi,
In my testing, I find that dcmdump is slightly faster than dicom_hinfo.
I ran 10,000 dicoms with:
dicom_hinfo -tag 0008,103e 00001.dcm
vs
dcmdump --print-short --search 0008,103e 00001.dcm
dicom_hinfo = 183 seconds
dcmdump = 145 seconds
But we should look into updating dicom_hinfo for the entire field and not just the first word.
thanks, Justin
by
discoraj
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AFNI Message Board
Hi,
The cluster linkage methods are what is used to calculate hierarchical clustering.
It basically rearranges the data based on dissimilarities of the regions.
The descriptions of the methods are here:
https://stat.ethz.ch/R-manual/R-devel/library/stats/html/hclust.html
There are also a links to the descriptions in the shiny app below the drop down selectors.
For the many ROI problems,
by
discoraj
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AFNI Message Board
Great!
If you make some pretty graphs that you can share, can you post them here?
by
discoraj
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AFNI Message Board
Hi,
Thanks for finding that bug for me!
It is fixed and will be in the next version update.
But if you need it now, you can download a fix here:
http://afni.nimh.nih.gov/pub/dist/data/shiny_temp/global.R
You should right click the link and "Save As".
Then use that "global.R" to replace the previous one in your abin folder (or wherever you put afni)
<where afni l
by
discoraj
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AFNI Message Board
Hi,
Is there only one file in the folder?
And what is the name of the file?
Thanks, Justin
by
discoraj
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AFNI Message Board
HI,
Sorry for the problems.
For the @afni_R_package_install -shiny
The default repository is .
But if for some reason, you can't reach that, you may have to install separately with another repository.
You can do that manually in R with:
install.packages(c('shiny','shinydashboard','plotly','colourpicker','data.table','gplots
by
discoraj
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AFNI Message Board
Hi,
There are probably lots of ways to bust them...
The tutorial web page has some of the caveats:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/ClusterExplorer/Introduction.html
I hope that helps some.
If you need anything, let me know.
Thanks, Justin
by
discoraj
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AFNI Message Board
hi,
Can you post the ClustExp_StatParse.py command you used?
The parentheses seems to be the problem here:
(Intercept)_F_p_uncor_0.005
Thanks, Justin
by
discoraj
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AFNI Message Board
Hi,
Cluster Explorer Intro Tutorial
There is a new set of scripts to help explore your data!
The scripts are included in the latest binaries.
The tutorial link (above) has more information and some basic steps to get started.
Post any problems, questions, or suggestions in this thread if you like.
The capabilities may be expanded in the future and it is rather new. So be kind.
Throw
by
discoraj
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AFNI Message Board
Hi,
Sorry to take so long to check back...
Another option (that I use) is 3dNetCorr.
with the -ts_wb_Z option
I find it a little faster if you have many ROIs.
thanks, Justin
by
discoraj
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AFNI Message Board
Quick link for Cluster Explorer example:
This will be gone shortly.
gone...
by
discoraj
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AFNI Message Board
Hi,
What commands did you use for the functional connectivity?
Can you post your code?
Thanks, Justin
by
discoraj
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AFNI Message Board
Hi,
If you want to start over, you can try:
https://afni.nimh.nih.gov/afni/community/board/read.php?1,156123,156123#msg-156123
Good luck, Justin
by
discoraj
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AFNI Message Board
Hi,
For the brave souls out there, here is a new afni install script for macOS:
Zipped:
afni_macOS_install_BETA.zip
Or more mac-ishly:
afni_macOS_install_BETA.dmg
It is still in beta and has been tested on macOS 10.12 and 10.13 (released 09/25/2017).
After downloading, just unzip the .zip or mount the .dmg
PLEASE PLEASE read the README first.
Then you can launch it installer with a
by
discoraj
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AFNI Message Board
Hi,
What is the input data?
Is it a single subject time series?
and the output that you want is a data set that can be thresholded in the afni gui?
Can you send the 3dinfo -verb output for the 3dDeconvolve output dataset?
Thanks, Justin
by
discoraj
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AFNI Message Board
Hi,
You could try:
Skull strip the T1.
Align T1 to CT (whole head).
Apply transformation to the stripped T1.
Use that as a mask on the CT.
I hope that makes sense.
We can help further if it doesn't work.
Thanks, Justin
by
discoraj
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AFNI Message Board
Hi,
Can you post your .bash_profile and/or .bashrc files from your home directory?
And it looks like you use fink and homebrew? Is that correct?
thanks, Justin
by
discoraj
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AFNI Message Board
set cx = 0
set cy = 0
set cz = 0
set width = 20
3dcalc -a template+orig -prefix roi \
-expr "and(rect((x-$cx)/$width),rect((y-$cy)/$width),rect((z-$cz)/$width))"
this worked as well.
Thanks!
by
discoraj
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AFNI Message Board
Hi,
I am trying to make a cube with edges of 7mm with the center at a specific coordinate.
Any thoughts on how to do it?
I was thinking of 3dUndump, but radius only does spheres.
Thanks, Justin
by
discoraj
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AFNI Message Board
Hi,
Step 5 may have to be changed to 5.3.0 or whatever the latest version is from time to time.
by
discoraj
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AFNI Message Board
What do you think about band pass settings for a TR of 1 sec?
We are doing resting state for functional connectivity.
by
discoraj
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AFNI Message Board
Hi,
Thanks!
Both options work!
Are there any other pitfalls I should look out for with the CMRR prisma sequences?
The 1 sec TR, 2mm resolution and number of slices seem like a whole new world.
Do the usual assumptions for blur kernel etc apply?
by
discoraj
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AFNI Message Board
Page 3 of 5
Pages: 12345