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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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Thanks - will keep that in mind!
I didn't see anything in the help message, which I found strange - but glad there are options for this.
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roopchansinghv
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AFNI Message Board
Yes - absolutely does!
The reoriented dataset, generated using the '3dresample' command you provided above, resulted in a dataset with no differences (as computed by 3dcalc) to the real-time data generated by Dimon - which should be the case, and what I hoped for!
Thank you Rick!
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roopchansinghv
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AFNI Message Board
Hi Folks,
We're in the process of updating several pieces of various pipelines, and one issue came up this morning.
We're transitioning our QA to be housed within an XNAT instance. Currently, AFNI datasets (time-series of EPI data) for the QA are generated in real-time by Dimon on our real-time PCs. However, when all data are already present in the XNAT instance, it seems to mak
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roopchansinghv
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AFNI Message Board
Hello
I thought a bit more about the images you sent, and then it struck me about how the warped B0 field maps overlaid on the original B0 field map.
I believe that the output field map from Siemens is not in radians. It is in scaled to span the full range of image units in Siemens DICOM (I believe either 0 - 4096, or -2048 to 2047. Someone else should confirm this).
If you look at the
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roopchansinghv
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AFNI Message Board
This looks good. From everything here, the only thing I've seen missing is some kind of field map smoothing / regularization. This was accomplished in our GitHub repository using the '3dmerge' command in the 'afniB0' function in the 'distortionFix.py' file.
If your input phase maps above (i.e. 'gre_fieldmap_phase') are already smoothed/regularized
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roopchansinghv
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AFNI Message Board
Hello,
The unit of Hz/s was chosen as it would give an easy way to scale the field offset, without having to pass along the additional parameter of the echo-time difference used to generate the B0 map. This was not for "GE data." This was a custom sequence written by me to generate B0 map data. Frequency to radians (per second) is a trivial scaling (lines 352 - 357 in this file).
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roopchansinghv
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AFNI Message Board
Hello,
I am responsible for most of the content of this repository, and got guidance implementing the distortion correction tools from various members of the AFNI team.
The B0 correction module using AFNI tools runs from approximately lines 250 to 300 in the "distortionFix.py" file.
The input to this module are a BIDS ID for 1 subject's data for a given session, the magnit
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roopchansinghv
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AFNI Message Board
I just pulled the most recent version of the AFNI source code, and compiled it for my El Capitan OS X machine.
Running:
make totality
was mostly uneventful, except I did not get any of the python scripts (in afni_src/python_scripts) copied over to the installation target directory. Is this something that should be done manually, or is there another build/install target that should be
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roopchansinghv
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AFNI Message Board
The Singularity folks have started dipping their toes into the water in terms of getting it working on OS X. This will still be via a Virtual Machine. But if you are already running, or are comfortable running the "Brew" software installation suite, there's the start of a procedure at:
I've not tested this myself, and it does not seem to be as self-contained and as
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roopchansinghv
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AFNI Message Board
I made another attempt at a full build over the weekend, using MacPorts' 4.9 version of GCC.
The tarball of AFNI from Jan 26 built fine, even without having to fix the inlined function definitions, or the void return in Dimon. Installing MacPorts' openmpi-gcc49 port seemed to let everything compile properly, with OpenMP. 3dAllineate's help message even had the correct number o
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roopchansinghv
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AFNI Message Board
Thanks - that worked perfectly!
A couple of other caveats with compiling AFNI with clang:
- There was an error in Dimon.c where a non-void function (make_sorted_fim_list) was not returning a value (turns out one of the returns in that function did not have a value).
- I had to disable openmp when compiling with clang. The error was not finding omp.h, but till I figure out how to g
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roopchansinghv
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AFNI Message Board
Hi All,
I've been trying to build AFNI on a Yosemite + MacPorts machine. I started with a functioning 10.8 Makefile, and on the first pass through, I got this error when trying to build the main AFNI binary:
/bin/rm -f afni
/usr/bin/gcc -O2 -m64 -DDARWIN -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -DDONT_USE_MCW_MALLOC -o afni afni.o afni_func.o afni_widg.o afni_warp.o afni_fim
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roopchansinghv
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AFNI Message Board
Hi All,
I was checking through a few routines, but could not determine if there was a function or macro to check if one data set was in the same space, on the same grid, and had the same orientation as another? Or is it a matter of doing something along the lines of:
if ( (ds1->daxes->nxx == ds2->daxes->nxx) &&
(ds1->daxes->nyy
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roopchansinghv
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AFNI Message Board
With the spiral sequence, you should also have gotten reconstruction software, along with instructions on how to use them. Such software will usually output DICOM or NIFTI-formatted data, and can be rather specific for the sequence data it reconstructs.
Reconstruction of images from scanner vendors' raw data usually requires proprietary information from the vendors. Software like this i
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roopchansinghv
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AFNI Message Board
Rick,
I meant external support for openSUSE 11.4. Many of the software repositories we use are being deactivated for this version, and I think only critical security fixes are being done now. The NIH 11.4 machine that produces those binaries are one of mine, and will be updated as well. But we would like to stay current with tools, libraries, etc - so we will be updating ...
I should cor
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roopchansinghv
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AFNI Message Board
Hi All,
We're in the process of updating our openSUSE machines that are currently running 11.4 (which is no longer supported). When trying to compile the AFNI source tree I downloaded this morning, I got the following error:
suma_datasets.h:727:13: warning: 'NI_GOT' defined but not used [-Wunused-variable]
gcc -std=gnu99 -shared -L/usr/local/lib64 -o R_io.so R_io.o -L. -L/u
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roopchansinghv
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AFNI Message Board