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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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Hello -
I have a (hopefully) simple statistics question. I have a dataset of reconstructed microelectrode recording sites across patients within the subthalamic nucleus (STN) - for each recording/site, I have a statistic for two analyses (testA and testB). What I want to understand is whether testA or testB values vary by anatomical location within the STN (is testA higher in one part, and tes
by
pmlauro
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AFNI Message Board
and to further clarify, my ultimate question is whether statistical values are observed above chance in specific voxels within the entire recording site blob
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pmlauro
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AFNI Message Board
Hello -
I'm plotting data from microelectrode recordings into anatomical space. Because patients can have variable recording sites, the spatial density of all plotted statistical is unequal. How can I test whether my plotted statistical values are observed above chance, while accounting for the variable number of recordings/samples at each voxel?
If it clarifies things, I have the data
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pmlauro
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AFNI Message Board
Hello -
I've noticed a small bug across functions (3dcalc, 3dMean). Whenever I set the -prefix argument as "some_dir/output.niml.dset", the output ignores the directories in the prefix, and simply outputs to the current working directory (./output.niml.dset).
Am I doing something wrong? Again, I've only noticed this with *.niml.dset or *.1D datasets, not *.nii or *+orig
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pmlauro
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AFNI Message Board
Yes, I registered each patient's electrodes to their std.141.* surface before mapping them all on the std.141.MNI* surface.
Thanks again!
Pete
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pmlauro
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AFNI Message Board
Ah! It hadn't dawned on me how I can use AFNI 3d* commands with *.niml.dset objects. Noice.
After performing 3dVol2Surf with each patient's electrodes to the standard MNI surface, I combined them with:
3dcalc -a s00_lh_ecog.niml.dset -b s01_lh_ecog.niml.dset -expr 'a+b' -prefix all_lh_ecog
I then plotted that on the standard MNI surface, and it's exactly what I
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pmlauro
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AFNI Message Board
Hi Rick -
Thank you for the quick response. So if I understand you correctly, in order to display all electrodes at once on a standard surface, all electrode coordinates should be warped to a standard space (MNI). From there, I can then run 3dVol2Surf on the collective MNI electrodes.
Pete
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pmlauro
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AFNI Message Board
Hello -
I'm working with some ecog data, and I'd like to display the results from all electrodes on a standard freesurfer brain.
I ran recon-all on each subject's T1 volume in their native space, and I then mapped each patient's CT-based electrodes to their native T1 volume using Trotta et al.'s (2017) software toolkit.
Now I would like to display the combined de
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pmlauro
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AFNI Message Board
Hello -
I have a series of T1w volumes with gadolinium signal present...and I'm having difficulty registering them to an atlas volume (AFNI_18.0.26, auto_warp.py, MNI_T1_2009c+tlrc). Specifically, 3dQwarp seems to interpret the vessels as 'brain,' and wraps them around cortical folds. Is there any principled way to remove the gadolinum signal, while sparing brain?
Thank you,
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pmlauro
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AFNI Message Board
Thank you for the clarification Paul!
...and many thanks for the new fat_proc* scripts. They are game-changing.
Pete
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pmlauro
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AFNI Message Board
Hello -
I'm currently using the 'fat_proc_imit2w_from_t1w' function to convert T1ws to imitation T2ws for DIFFPREP structural registration. Reading AFNI helpfile for the function explains:
NB: if you use a volume made this way as a reference in TORTOISE,
then at least for ~adult-human-like (imitation) t2w volumes, at
present it seems like you should use the option:
by
pmlauro
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AFNI Message Board
Hello AFNI friends -
I've been using auto_warp.py/3dQwarp quite a bit lately for both subject->atlas and within-subject (2 separate timepoints) registration, and I'm a big fan. I have some questions about the output however -
1) In the anat.un.aff.qw_WARP.nii volume, what do the voxel values in each sub-brick (x_delta, y_delta, z_delta) refer to? Is it an arbitrary 'shift
by
pmlauro
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AFNI Message Board