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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
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Thanks for the info.
On my system, dicom_hinfo was a bit faster than dcmdump when run in a "foreach" loop in c-shell. However, I just discovered that dcmdump can read multiple dicom files at once, so that will speed things up a bit.
Best,
Rasmus
by
rbirn
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AFNI Message Board
Hello,
I'm in the process of writing a script to sort & rename lots of dicom files based on information in the dicom header. Ideally I wanted to include the series description (dicom field "0008,103e") as part of the output directory name (with spaces replaced with underscores, using sed). However, dicom_hinfo only returns the first word of the series description. I could us
by
rbirn
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AFNI Message Board
Hi AFNI gurus,
Is there an AFNI program for randomly reshuffling time series data, independently for each voxel? I'd like to use this to estimate the null distribution for the correlation between a seed region and other voxels in the brain (i.e. functional connectivity) in one of my datasets. Alternatively, is there a program that can help me estimate such a null distribution?
Thanks,
by
rbirn
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AFNI Message Board
Ignore my previous comment, I figured it out.
My commands to achieve what I want are now as follows:
If my original dataset is named t2.nii and the nudged dataset it t2_nudge.nii, then I extract the transformation matrix of that nudge as follows:
set nudge_string = `3dinfo t2.nudge.nii | tail -2 | head -1 | awk -F: '{print $NF}'`
3drotate $nudge_string -prefix tmp.rot.t2 t2.ni
by
rbirn
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AFNI Message Board
It looks like the transformation matrix is the same (ROTATE_MATVEC_000000 vs. ALLINEATE_MATVEC_S2B_000000), but the dataset from 3drotate specifies a ROTATE_CENTER_OLD and ROTATE_CENTER_BASE.
What I'm really trying to do is process some infant MRI data which were acquired with the head in a quite oblique orientation relative to the slices. As a result, the automatic warping to the templa
by
rbirn
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AFNI Message Board
Hello AFNI gurus,
I'm trying to convert a rotation specified by "-rotate -38I 0R 0A" to a matrix that I can apply to another dataset. I tried the following:
cat_matvec -ONELINE '-rotate -38.00I 0.00R 0.00A' -I > xform_test.aff12.1D
3dAllineate -1Dmatrix_apply xform_test.aff12.1D -master t2.nii.gz -prefix test.3dAllineate.nii.gz t2.nii.gz
however, when I
by
rbirn
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AFNI Message Board
Hello,
Is there a script or program that can tell me is a dataset is complete & loadable? I was running a script and my disk ran out of space. As a result, several partial datasets got created. Since I'm using compressed datasets (BRIK.gz), it's not easy to just go by file size. I can of course remove all of the files and rerun everything, but it would save me some time if I coul
by
rbirn
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AFNI Message Board
Hello,
This post was originally a question regarding AUTO_GZIP, but I figured it out.
Apparently NIFTI files get automatically gzip'ed when AFNI_COMPRESSOR = GZIP is set even when AFNI_AUTOGZIP is set to NO. (AFNI BRIK files follow the AFNI_AUTOGZIP logic).
Best,
Rasmus
by
rbirn
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AFNI Message Board
Hello,
I am getting strange behavior when running 3dcopy on some of my data files. The data is originally in LSB_FIRST. 3dcopy changes it to MSB_FIRST, and the image appears byte-swapped in the AFNI viewer. When I use 3dcalc (3dcalc -a Anat_1+orig -expr 'a' -prefix Anat_1_calc), then the byte order is MSB_FIRST but the data appears okay in the viewer.
3dcopy is used by align_
by
rbirn
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AFNI Message Board
Congratulations, Bob! Brings back a lot of memories. Looking at multiple slices at once! Performing Talairach transformations "manually," writing plugins, having to worry about color bit depth on the old unix machines, seeing the introduction of a "bucket" data set type, ... Lots of fun. And AFNI is a way cooler name than FD3! :)
by
rbirn
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AFNI Message Board