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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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The mask was made in FSL with "mni152_t1_2mm_brain," which I believe uses the MNI152 NLIN 6th Gen asymmetric template. If I want my processed EPI data to fit this template, what afni template would I use for SSwarper and input to the -tlrc base option in afni_proc.py?
by
Daniel Zhu
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AFNI Message Board
I've run it just now and got:
-- no warnings for correlation matrix (cut = 0.400) --
Would it be relevant to mention that I'm running this on resting-state fmri data? I've used the -GOFORIT and -Rwherr options and am using the output from that as the final epi dataset. Is that an appropriate usage of 3dREMLfit for removing temporal autocorrelation in resting state data?
by
Daniel Zhu
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AFNI Message Board
Hi,
I'm trying to perform seed-based functional connectivity analysis, but I noticed that the grid size of the processed epi data from running afni_proc.py are different from those of my seed mask. The mask is in MNI space with dimensions of 91x109x91 2mm voxel size, but the processed epi that results from proc.py is 96x114x96 2mm.
By my understanding, the grid size of the final epi da
by
Daniel Zhu
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AFNI Message Board
Hi Daniel,
After orienting the epi data, I reran my preprocessing through afni_proc.py. I want to do pre-whitening through 3dREMLfit, but I'm getting the following error:
3dREMLfit -matrix X.xmat.1D -input pb04.sub_id.r01.scale+tlrc.HEAD -fout -tout -Rbuck stats.sub_id_REML -Rvar stats.sub_id_REMLvar -Rfitts fitts.sub_id_REML -Rerrts errts.sub_id_REML -verb
++ 3dREMLfit: AFNI versio
by
Daniel Zhu
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AFNI Message Board
Thanks Daniel!
I'll follow through what you've done, check out the results, and come back if I have any other concerns. The different orientations was my original intuition as well - awesome that I know how to fix it now.
by
Daniel Zhu
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AFNI Message Board
Hi,
I ran across a alignment issue as well between epi and anatomical. I don't have much experience with brain imaging, in fact this is one of my first projects, so I would totally appreciate some help. I ran the afni proc with the lpc+ZZ cost function and giant move and saw the following results:
After looking at the epi and anatomical raw data, I noticed that they have different
by
Daniel Zhu
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AFNI Message Board
Hi Rick,
Thanks for the corrections. How would you recommend that I proceed to blur only in the gray matter mask? One way I have tried is going into the output script and changing the Mmask parameter in 3dBlurInMask to the gray matter mask produced by afni, but I'm not sure if this the best way.
On another note, I noticed that the GM mask created by afni does not have as many voxels as
by
Daniel Zhu
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AFNI Message Board
Hi, upon reviewing the output script generated by afni_proc.py, I noticed that the options for 3dBlurInMask were not what I expected. I'm trying to blur only in the gray matter eroded mask with a fwhm of 5.0 mm. The following is the afni_proc.py script:
afni_proc.py -subj_id $subj \
-script proc.SS.$subj -scr_overwrite \
-blocks
by
Daniel Zhu
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AFNI Message Board