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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
You may need to reinstall XQuartz and then reboot (or login and logout). XQuartz really needs that login/logout sequence to be recognized.
by
Peter Molfese
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AFNI Message Board
Try changing Inputfile to InputFile (capitalize the F).
by
Peter Molfese
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AFNI Message Board
You may also need to remove the two blur estimates as surface-baesd analyses blur to a set FWHM instead of adding blur.
-regress_est_blur_epits -regress_est_blur_errts
by
Peter Molfese
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AFNI Message Board
If you are not looking for session to session changes in cortical measures, then Freesurfer is pretty good at aligning multiple anatomical images and can use the two (or more) to do a type of anatomical motion correction. In the end you'll end up with only one SUMA directory for use in the surface-based analysis pipeline.
No need to align or skull-strip outside of Freesurfer - in fact
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Peter Molfese
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AFNI Message Board
It looks like it's still finding the libraries in /usr/local/lib. It may be that you need to move the folder using:
sudo mv /usr/local/lib /usr/local/lib.save
I'm fairly certain that MacOS X doesn't install anything in /usr/local by default, so you shouldn't break anything that is built into the OS.
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Peter Molfese
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AFNI Message Board
Odd. Can you run the otool command on 3dAllineate or 3dQwarp?
otool -L /Users/NEURO-222/afni/3dAllineate
Details here:
http://afni.nimh.nih.gov/afni/community/board/read.php?1,141493,141579#msg-141579
by
Peter Molfese
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AFNI Message Board
Two things to try:
1) Try it in a new window
2) What's the new output of afni_system_check.py -check_all?
by
Peter Molfese
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AFNI Message Board
Hi Barbara,
I've seen the libgomp error quite a bit recently. I'm guessing that you have the Enthought Python distribution installed, which can cause some interesting issues.
Try moving /usr/local/lib to /usr/local/tmp.lib and running the programs again. Let me know if this works.
Peter
by
Peter Molfese
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AFNI Message Board
That's curious, it looks like AFNI is not on your PATH. A few questions:
1) Are you launching the program by just typing 3dQwarp at the prompt or are you providing the full path?
2) Have you followed the instructions on this installation page?
3) What is the output of:
which afni
I suspect that you are launching the application directly and need to add the AFNI directory to
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Peter Molfese
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AFNI Message Board
Hi Barbara-
What is the output of the following command?
afni_system_check.py -check_all
by
Peter Molfese
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AFNI Message Board
I would follow Daniel's example to do something like this, assuming you have a 2 second TR.
3dTcat -prefix segment1 alldata+tlrc.[0..119]
3dTcat -prefix segment1 alldata+tlrc.[120..239]
3dTcat -prefix segment1 alldata+tlrc.[240..359]
3dTcat -prefix segment1 alldata+tlrc.[360..480]
With only four segments, it may not be worth more complex scripting. I would suggest using afni_proc
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Peter Molfese
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AFNI Message Board
3dTshift will try to use information in the header to "guess" the correct slice order. I believe that if this information is not available, 3dTshift will say something like "Slices already in order".
From the help:
By default, uses the
slicewise shifting information in the dataset header (from the 'tpattern'
input to program to3d).
You can check if the i
by
Peter Molfese
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AFNI Message Board
Outside of 3dcalc, you could use one of the 3dANOVA programs (if your design is balanced) or 3dMVM (if your design is not balanced).
by
Peter Molfese
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AFNI Message Board
If you believe the dataset with +tlrc is actually in subject space (and not transformed into some type of standard space: MNI/TAL), then you can change it via:
3drefit -view orig -space ORIG dataset+tlrc.
I'm not immediately recalling an option in .afnirc to force things to be +orig. I suspect you're going between NIFTI and AFNI file formats and occasionally other packages (SPM/F
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Peter Molfese
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AFNI Message Board
You are running a fairly old version of AFNI (2009). Have you tried updating?
I suspect the newer version may give you a more informative error message - or hopefully no error message at all!
by
Peter Molfese
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AFNI Message Board
Haskins Laboratories is seeking a Research Associate for projects related to Cognitive Neuroscience and Language/Reading Development as part of several recently funded NIH grants. Haskins is a leading community in the field of cognitive neuroscience, with opportunities to collaborate with leaders in the field of functional and structural MRI with access to a wide range of typical and patient pop
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Peter Molfese
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AFNI Message Board
As a possible alternative to having two button widgets (Overlay1, Overlay2), what about adding the functionality to select multiple overlays in the Open Dialogue listing the files. Something along the lines of either selecting multiple datasets (holding shift or control) or multiple apply and set buttons (one row below) to allow the second overlay to be active. I suppose you would need some ind
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Peter Molfese
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AFNI Message Board
This April Fools is almost as good as the claim that Netflix was bringing the TV show Firefly back...
Daniel Glen Wrote:
-------------------------------------------------------
> Because of all the confusion regarding coordinate
> order, AFNI packages will now be only
> 1-dimensional, something like k-space, so the
> physicists will like it. 1D programs will accept
> 3D da
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Peter Molfese
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AFNI Message Board
It could be that you have a AFNI version prior to afni_proc.py supporting the nonlinear warp. If the output of "afni -ver" appears out of date, I suggest you update your binaries using: @update.afni.binaries -d
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Peter Molfese
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AFNI Message Board
It's been a while since I've used fslmaths, but if I'm reading this correctly as you want a mask where the t-stat is exactly 10 and nothing else, you could do something like:
3dcalc -a stats.subj1+tlrc.HEAD'' -prefix subj1_masked_t10.nii.gz -expr 'equals(a,10)'
More details are available on the 3dcalc help page.
by
Peter Molfese
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AFNI Message Board
The AFNI workshop hosted by Haskins Labs and Yale University is May 27-30. Registration is open at: http://www.haskins.yale.edu/afni/
by
Peter Molfese
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AFNI Message Board
If you want a 3mm^3 resampling as opposed to a 333mm^3, change your command to be "-dxyz 3"
I suspect that adwarp is having a hard time creating a file with 333mm^3 voxels with your dataset. It should probably give an error message in that case, but I tested it on some files here and just get the usual output.
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Peter Molfese
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AFNI Message Board
I hit post and then saw that Daniel beat me to it!
3dresample will not warp your data to TT_N27 space, for that you will need to use another @auto_tlrc step. Assuming that your resting state data is already aligned with your anatomical data in subject space, you could do the following:
#warp anatomical to TT_N27 space
@auto_tlrc -base TT_N27+tlrc -input AnaT.nii.gz
#apply that warp to
by
Peter Molfese
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AFNI Message Board
I've had success using the -affter flag to concatenate the affine transform to 3dQwarp's nonlinear warp.
auto_warp.py -base TT_N27+tlrc -input anat+orig -skull_strip_input yes
3dNwarpApply -master ../TT_N27+tlrc \
-source MyROI.nii \
-nwarp '../awpy/anat.un.aff.qw_WARP.nii' \
-affter ../awpy/anat.un.aff.Xat.1D \
-prefix ROI_tt
by
Peter Molfese
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AFNI Message Board
There may be an even easier way, but you could create a mask from the cluster and then pass that mask to whereami. Here I say give me a mask with anything that has a t-value greater than 2.75, adjust numbers accordingly.
3dcalc -a 'Subject001+tlrc.' -prefix MyMaskOfActivation -expr 'ispositive(a-2.75)'
whereami -bmask MyMaskOfActivation+tlrc -atlas CA_N27_ML
You will
by
Peter Molfese
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AFNI Message Board
If you want something while the binaries update you could use sub-brick selectors or value selectors with 3dCM. If your input file has 20 values in a single sub-brick, you could do something like:
for aNum in {1..20}
do
echo $aNum;
3dCM MyROIs+tlrc."<$aNum>";
done
The link that I see for the no.fink binaries is
by
Peter Molfese
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AFNI Message Board
There is a really nice new-ish feature in 3dCM to do this for you:
3dCM -all_rois dset+tlrc.HEAD
by
Peter Molfese
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AFNI Message Board