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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 AFNI gurus!
This question JUST occurred to me - does the input provided to tpattern in 3dTshift assume axial acquisition? Or is alt+z2 referring to the order in which the slices were saved to disk as explained here (message #5)? In other words, if I have acquired interleaved slices but in the sagittal direction, can I still use alt+z2 for tpattern?
Can't believe I had never thoug
by
mrinmayik
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AFNI Message Board
Hi Paul,
Thanks a lot for this information. I'll give it a shot! And I think I'll uninstall PyQt4 after the workshop so I can continue to get the helpful output from matplotlib, etc.
We've been pointing attendees of our workshop to the AFNI documentation and YouTube channel in every session. So I'm sure you're going to get a bunch of views from Milwaukee in the next
by
mrinmayik
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AFNI Message Board
Hi Paul,
Hope you're well!
I need uber_subject.py for an "introduction to fMRI preprocessing workshop" I'm conducting, and thought a GUI would be useful to demonstrate how the "theory of preprocessing" they learned would translate to actually processing the data.
I'm having similar issues with starting uber_subject.py. I tried running uber_subject.py fr
by
mrinmayik
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AFNI Message Board
Hello AFNI Gurus!
I have extracted Hippocampal masks from participants' Freesurfer segmentations. I want to subdivide this ROI into thirds along the anterior-posterior axis (y-axis?). E.g., if a certain participant's hippocampus goes from slice 90 to slice 120 , I want the first ROI to go from slices 90-103, the second ROI to go from 104-117 and so on. I am using 3dAutobox to get the e
by
mrinmayik
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AFNI Message Board
Hi Paul,
Thanks a lot for your response!
Yes, I did use afni_proc.py to preprocess these people with the following blocks:
-blocks tshift align volreg mask blur scale regress
So the EPIs are never warped to standard space. The reason for this is because we're looking to do multivariate analyses in small regions that are hand-segmented in individual T1s, and we don't want to wa
by
mrinmayik
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AFNI Message Board
Hello AFNI Gurus!
I have some ROIs in MNI space that I would like to transform back to native space so that I can extract time-series from EPIs in native (i.e. non-normalised) space using these ROIs as masks. The participants' anatomies are normalised using SSwarper, and EPIs are aligned to the participants' native space anatomies using align_epi_anat.py through afni_proc.py.
I used t
by
mrinmayik
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AFNI Message Board
Hi again!
I have been using a computing cluster at our university to run 3dDeconvolve. Recently, I started working with a new dataset (EPI resolution 2x2x2mm) where I have to run trial-by-trial 3dDeconvolve models for 162 trials, and found that it is taking about 6 hours to run deconvolve per trial. In the past, I was able to bring down computation time by increasing the number of jobs specified
by
mrinmayik
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AFNI Message Board
Success!! Rick, I was able to generate the QC files by removing the "-radial_correlate yes" flag! Sorry- that was a stupid mistake. Thanks a lot!
Thanks for your suggestions, Paul. It does take a while for the admin folks to make cluster-wide changes to software versions, so installing these in my own path will make life much easier! I'll definitely do that.
Thanks again, for
by
mrinmayik
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AFNI Message Board
Hi again,
Paul, the data is being uploaded now- it should be done in an hour or so!
Rick- thanks for your suggestion! I assumed the "-radial_correlate_blocks" was an additional option passed to radial correlate block that was turned on with the "-radial_correlate yes" flag. I'm running a new iteration without the latter flag. I'll report back when it's done!
by
mrinmayik
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AFNI Message Board
Hi Paul,
Thanks a lot for your response!
Actually both the preprocessing and the apqc_make_tcsh.py command are being run using the same version of AFNI from 2 years ago (it's the one we have installed on our clusters). And the results folder does have a .json file in it. This is what is in that json file:
"afni_package": "linux_openmp_64",
"afni_ver&q
by
mrinmayik
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AFNI Message Board
Hello AFNI gurus!
I am running preprocessing on some data and was hoping to generate the the HTML quality control reports using:
apqc_make_tcsh.py -review_style pythonic -subj_dir . -uvar_json out.ss_review_uvars.json
as suggested here .
But I'm getting the following error:
++ Found 39 files for QCing.
** ERROR: radcor number of ulays (0) doesn't match number of olays (6)
Wh
by
mrinmayik
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AFNI Message Board
Thank you all, for your comments! I will convert thee 3dDeconvolve output to NIFTI before importing it into Matlab, then.
Milwaukee is hanging in there, Paul! Hope you are all well amidst all this craziness! :)
by
mrinmayik
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AFNI Message Board
Hi All,
I need to import certain sub-BRIKs of the output from 3dDeconvolve into a Matlab toolbox. Is there a way to write the sub-BRIKs into .mat files? I saw this afni matlab library (https://sscc.nimh.nih.gov/afni/matlab/). Is that what I should be using? Just wanted to check since it's an old page!
Thank you,
Mrinmayi
by
mrinmayik
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AFNI Message Board
Ahhhh yes! Sorry, I should've thought of that option!
I'll give it a shot.
Thanks a lot for your help!
Mrinmayi
by
mrinmayik
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AFNI Message Board
Thanks for your responses, Rick and Paul!
I am running the apqc_make_tcsh.py command from the $subj.results folder that is generated by the following afni_proc command:
afni_proc.py -subj_id $sid -script proc.$sid -scr_overwrite \
-blocks tshift align volreg mask scale \
-copy_anat $anat_ss
by
mrinmayik
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AFNI Message Board
Hi again!
I have a (not-so) follow-up question regarding the same afni_proc command above. I added the "-html_review_style pythonic" flag to the command, but it isn't generating any QC scripts (except for @epi_review.$subj) or the QC_$subj folder. I tried running the following command given here:
apqc_make_tcsh.py -review_style pythonic -subj_dir . \
-uvar_json out.ss_
by
mrinmayik
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AFNI Message Board
Hello AFNI gurus!
What is the best way to preprocess data such that I have slice-time corrected, aligned, motion corrected, scaled, and blurred EPIs in both the subject's native space as well as standard space? I need to run 3dDeconvolve in native space (to extract Betas for a Representational Similarity Analysis) and standard space (to do whole-brain group-level contrasts).
Using the f
by
mrinmayik
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AFNI Message Board