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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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I've uploaded the data.
dcm2niix does result in properly oriented images, but I'm hoping to3d will as well since it's incorporated into a lot of our legacy scripts.
Thank You!
-Chad
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Chad N
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AFNI Message Board
So changing the acquisition direction seems to orient the images properly:
Per-frame Functional Groups Sequence (5200,9230)
>Plane Position Sequence (0020,9113)
>>Image Position (Patient) (0020,0032) = -96.313\-89.5543\-73.0048
>Plane Orientation Sequence (0020,9116)
>>Image Orientation (Patient) (0020,0037) = 1\0\0\0\1\0
>Pixel Measures Sequence (0028,911
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Chad N
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AFNI Message Board
Hi,
I've got some Enhanced MR images that are coming through flipped I-S after to3d.
I can fix the anatomic series by including the -oblique_origin flag. The fMRI and DTI series remain flipped even if I use that flag.
These are from a Siemens Vida 3T scanner. What is the best solution for using Enhanced MR formatted images with AFNI? Will changing the acquisition direction make a di
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Chad N
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AFNI Message Board
The open source GDCM (http://sourceforge.net/projects/gdcm/files/gdcm%202.x/) also has a good data dictionary under Source/DataDictionary/privatedicts.xml
It has much more than just GE.
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Chad N
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AFNI Message Board
Thanks Daniel,
That works great, but flips the anatomic upside down in the sagittal and coronal view.
3dWarp -card2oblique anat+orig singleslice_epi+orig
Seems to work as well; then I can use the original anatomic as the underlay and the warped single slice as the overlay.
Thanks Again,
-C
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Chad N
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AFNI Message Board
I have some single-slice data that I want to overlay on an identically oriented anatomic image (identical image position (patient) DICOM attributes). If I just do to3d on the slice data and anatomic, the single slice data is not located in the correct spatial location
If I deoblique both volumes, the data is positioned correctly, but the single-slice is (as expected) now a series of strips
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Chad N
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AFNI Message Board
My fault. They are identical once I make the changes to the waveform file (and make it not read-only...sigh...).
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Chad N
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AFNI Message Board
I am trying to recreate some old data (hence using the old 3dfim+ program), but I'm noticing some significant differences between:
3dfim+ -input 'prmasked+orig[2..$]' -polort 2 -ideal_file ideal.1D -out Correlation -out '% Change' -out Baseline -bucket prfinal
and
3dfim+ -input prmasked+orig -nfirst 2 -polort 2 -ideal_file ideal.1D -out Correlation -out '
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Chad N
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AFNI Message Board
Thanks Ziad. It's available in the openmp binaries.
We have a bunch of Red Hat 5.x boxes in the lab that don't like the openmp binaries very much, so we usually use the xorg7 binaries on everything. This Fedora box can handle the openmp ones, though, so I should be set.
Cheers,
-Chad
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Chad N
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AFNI Message Board
$ afni -version
Version AFNI_2011_12_21_1014
[]
Should have provided that earlier...
-C
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Chad N
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AFNI Message Board
This is great, Paul. On first pass, it looks like 3dTrackID worked like a charm -- do we have to use the -sep_dsets in 3dDWItoDT, or will 3dTrackID accept a single brick file (like the default from 3dDTeig)?
Also FYI, I updated my binaries this morning and noticed that 3dProbTrackID was not downloaded (linux_xorg7 package). Further, 3dDWUncert would not run without the gsl libraries (easy to
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Chad N
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AFNI Message Board
Depending what you're end goal is, I know Prism Clinical Imaging (link) has an AFNI-friendly viewer that can do multiple overlays and export them as JPEG/PNG/DICOM.
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Chad N
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AFNI Message Board