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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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Hi Daniel,
I appreciate your reply! Unfortunately, we didn't have contrareg output from our FreeSurfer processing, and rerunning FreeSurfer wasn't an option. Good to know about this for the future though. Sounds like that would be a more straightforward solution.
What I've implemented instead is a process relying heavily on SurfDist to measure distances along the meshes. Fir
by
benconrad
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AFNI Message Board
Hello AFNI gurus and community,
I am interested in comparing some surface data between the left and right hemispheres at the node level. I think the method described in Jo et al. (2012) https://doi.org/10.1371/journal.pone.0048847 is precisely what I need, where they find the left/right node-to-node correspondences based on distance to anatomical landmarks. Given Drs. Cox and Saad are coauthors
by
benconrad
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AFNI Message Board
Hi Gang,
This is not the case. These voxels have data for all subjects. No masking has been applied at the subject level (aside from the EPI extents mask). Regardless, I have been using the option -missing_data 0 when running 3dMEMA, so I don't think that's the issue.
-Ben
by
benconrad
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AFNI Message Board
Hello again,
I have a new, though potentially related, issue with 3dMEMA output (if you all think this should be a separate post, happy to do that). This time the group-level t-stat maps from 3dMEMA are showing several clusters with a value of 100.
These areas are locations with the highest group-level coefficients, but they should not be t-values of 100.
These maps are derived from scaled d
by
benconrad
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AFNI Message Board
Hello AFNI gurus,
A minor question and observation. Why did the default EPI masking in afni_proc.py change from applying 3dAutomask with dilation of 1 voxel to using no dilation? I noticed this while comparing coverage maps from two different datasets, one processed with a more recent version of AFNI in which the dilation is not applied, and just want to be consistent (easy enough to rerun 3dA
by
benconrad
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AFNI Message Board
After scaling, as expected, the subject-level t-maps remained nearly identical (seemingly within rounding error). The effect estimate map from 3dMEMA group-level analysis now looks correct (see attached screenshot). The group-level t-values and clusters change a bit, but presumably more correct since the subject-level betas are more meaningfully comparable. Thanks Gang!
-Ben
by
benconrad
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AFNI Message Board
Ok, I understand. I will reprocess with scaling and report back. Thanks for the additional reference and for your support!
-Ben
by
benconrad
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AFNI Message Board
Hi Gang,
I did include the option "-missing_data 0" in the 3dMEMA script. And, after checking some of the values, I don't seem to see any strong outliers. The attached png shows boxplots for subject-level coefficients from the contrast of interest, extracted from three voxels (two from motor cortices and one from fusiform area). These voxels are capped in the 3dMEMA output. Also
by
benconrad
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AFNI Message Board
Hello,
I recently used 3dMEMA for a simple group analysis looking at activation differences between two conditions within one group (e.g. "StimA-StimB"), and followed the pipeline described here . Things have worked as expected (thank you for publishing this script!). However, in the output statistical maps, in areas where there are strong effects, the estimated beta values appear to
by
benconrad
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AFNI Message Board
Hi Rick,
I updated my binaries and things worked as expected. Really appreciate the support! Thank you!
-BC
by
benconrad
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AFNI Message Board
Hello,
I have an issue with align_epi_anat.py which I think I have traced back to the source of the error. Perhaps it is a syntax error. I ran into issue originally during afni_proc but am able to reproduce using only the align_epi_anat.py command as below:
align_epi_anat.py -anat2epi -anat
\
> Price_234469.17.01.17-40-09.WIP_T1_MPRAGE.01+orig \
>
by
benconrad
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AFNI Message Board