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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 Jeremy -
My vote would be to use 3dTcat to break them into individual TR files, and then 3dZcutup to slice up the individual slices. Then reassemble with 3dZcat and 3dTcat. You can also use 3dTsplit4D in place of the initial 3dTcat.
-Peter
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Peter Molfese
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AFNI Message Board
Thanks for that! I would suggest you update XQuartz to the newest version and restart your machine. That should fix it. But let me know!
Also looks like homebrew may need to either update or reinstall.
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Peter Molfese
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AFNI Message Board
Hello,
Could you post the output of the following command?
afni_system_check.py -check_all
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Peter Molfese
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AFNI Message Board
Hello,
Thanks for posting the script. Any chance of posting the alignment photos on google as well?
It appears that you used a pretty old version of afni_proc.py to generate the script (2014), so I would first suggest updating your version of AFNI. For the alignment, I suspect that adding "-giant_move" to your align_epi_anat step would fix the issue or in the original afni_proc
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Peter Molfese
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AFNI Message Board
Hello,
Partial volumes are tricky... You shouldn't need 3dresample. Are the results aligned before the 3dresample step?
A few other ideas if the results are misaligned before 3dresample:
1) If your DWI image lacks good contrast/detail/texture, you can try the mutual information cost function.
2) try and nudge the volumes closer and use 3dAllineate directly.
3) use ITK-SN
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Peter Molfese
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AFNI Message Board
Hello,
Having the script would be helpful. Could you try to copy and paste the text into a code field in the response box?
-Peter
by
Peter Molfese
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AFNI Message Board
Just curious if there are some network properties that we could also use to debug things:
1) You're using MacOS?
2) What protocol is the network share? NFS? SMB? AFS?
3) How big are the files?
4) Can you try unsetting AFNI_COMPRESSOR and setting AFNI_AUTOGZIP to NO?
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Peter Molfese
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AFNI Message Board
Hi Maya-
I generally haven't had any trouble getting it into MNI space. Can you post what commands you've tried (the actual syntax)? That'll help us debug here.
-Peter
by
Peter Molfese
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AFNI Message Board
Hello,
Please see this thread on how to adjust for the same issue and solution:
Quoteusers should subtract ~TR/2 from the stimulus times (actually (N-1)/N * TR/2 s, assuming N slices are evenly distributed over the TR), but TR/2 is close enough if there are many slices.
-Peter
by
Peter Molfese
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AFNI Message Board
There are some options within AFNI for nonparametric statistics, see here.
And the bayes approaches can be found here, here, and here. Although i may have missed a link or two.
Is there a specific thing you're hoping to do with your data that requires non-parametric statistics?
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Peter Molfese
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AFNI Message Board
Hmmm... plenty of things that could be causing the header to go wonky. I wonder if you could use matlab's niftiwrite function to write a NIFTI that we could then read into AFNI.
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Peter Molfese
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AFNI Message Board
It's true that throwing more processors at each subject with afni_proc.py has limited impacts on overall processing time. Some programs (3dREMLfit, 3dClustSim, 3dAllineate, 3dQwarp) do take advantage of OpenMP for using multiple processors. You can set how many threads that they use with the environmental variable OMP_NUM_THREADS, with the sweet spot (in my experience) being around 12 CPUs.
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Peter Molfese
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AFNI Message Board
I agree with Josh on this... The error being produced is from FSL's flirt, so you should probably check with them...
I will say that this script is somewhat problematic in the following ways:
1) you're using 3dvolreg with the -tshift option, which is convenient but you probably also should to slice timing correction in 3dTshift in case your file doesn't have the slice informa
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Peter Molfese
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AFNI Message Board
Looks like you have some NAN values in your physio file. Interpolating those took care of the first issue for me. But another error is caused due to having a trigger column but no cardiac column in your json/tsv.gz files.
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Peter Molfese
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AFNI Message Board
EDIT: I originally thought this option would also forego the EPI strip, but apparently it doesn't having just tested it.
-anat_has_skull yes/no : specify whether the anatomy has a skull
e.g. -anat_has_skull no
Use this option to block any skull-stripping operations, likely
either in the align or tlrc processing blocks.
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Peter Molfese
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AFNI Message Board
Try:
1dplot -ok_1D_text test.1D{1..$}
That will turn the labels into 0's and then ignore that first row (of now zeros) in the file.
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Peter Molfese
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AFNI Message Board
Preprocessing makes a HUGE difference in any type of analysis. And so you'd want to try and match these as closely as you can. Perhaps trying to use preprocessed data from CONN in AFNI or AFNI's proc.py data in CONN.
Beyond preprocessing, there are differences in how CONN and AFNI handle significance testing. CONN has options for Random Field Theory (RFT) and other methods, wherea
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Peter Molfese
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AFNI Message Board
Partial volumes are often tricky based on the content of the slab and contrast. Seems like you've tried most of the ways I've used in the past to get alignment. Can you post some screenshots and perhaps send me a PM to download the data?
Some have found this blog post to be helpful:
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Peter Molfese
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AFNI Message Board
I would recommend using the original anat for Freesurfer's recon-all. They have their own normalization scheme that suits their segmentation quite well.
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Peter Molfese
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AFNI Message Board
EDIT: Rick responded with deeper knowledge on how 3dDeconvolve does things and after me debating this with him several times, I'll direct you to his response below.
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Peter Molfese
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AFNI Message Board
I'll echo Gang's answer about using the residuals from 3dMVM as likely the best option.
Years ago, 2014 apparently - I did a similar approach to what you proposed of estimating smoothness with 3dFWHMx in this paper:
That was of course early in the entire cluster exploration process and would still say is a valid approach, especially if you're conservative in your cluster s
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Peter Molfese
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AFNI Message Board
My recommendation is to reprocessing using Subject_SurfVol.nii as your "anat" dataset in afni_proc.py with the -anat_has_skull set to "no". Then make sure that you have things aligning to the anatomical via -volreg_align_e2a. I've found this is generally the safest and also benefits from all of the AFNI automated QC images.
As an alternative, you can use @SUMA_Alig
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Peter Molfese
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AFNI Message Board
Noticed that you said you aren't normalizing the data to MNI or standard space. You can still use this approach by taking those atlas regions back to subject space using the inverse transform out of auto_warp.py or @SSWarper.
If you use the Freesurfer segmentation, those are already in your subject space after you run @SUMA_Make_Spec_FS - though the principle is pretty similar and the
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Peter Molfese
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AFNI Message Board
Hi Mpark-
You have a few options. The main two that come to my mind are:
A) Take the large ROI and divide it into multiple ROIs using at Atlas.
Many ways to do this, but to divide this into the most simple steps: 1) use whereami to create an ROI of an atlas region / Freesurfer segmentation. Repeat this step for Left and Right and any other sub-regions you'd like 2) Use Clusteriz
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Peter Molfese
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AFNI Message Board
In case you haven't tuned in yet, stream the workshop here:
You can also jump to each speaker within the stream using the following links:
Chris Baldassano -
Elizabeth DuPre -
Janice Chen -
Gang Chen -
Emily Finn -
Javier Gonzalez-Castillo -
Jeremey Manning -
Carolyn Parkinson -
Elizabeth Redcay -
Monica Rosenberg -
Tammy Vanderwal -
Uri Hasson -
Don't for
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Peter Molfese
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AFNI Message Board
It can go most places in the script. I usually put it near the volreg_* steps and before the blur_size. You'll want to tell the script that it's an add-on to the align_epi_anat.py by giving it the -align_opts_aea flag first. Example below.
-align_opts_aea -giant_move
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Peter Molfese
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AFNI Message Board
Yes, the NIFTI header extension (separate from the AFNI info) seems to be throwing off the AFNI viewer. Once you remove the header you should be able to see the slice timing in the graph view of AFNI like Andy demonstrates.
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Peter Molfese
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AFNI Message Board
And yes, that should work just fine. Except that it looks like the text file (test45.1D) isn't representing the altplus/alt+z timing information. Instead it just goes from slice 1 to slice 45 in an ascending way.
So if the data is actually ascending you could use -tpattern seqplus. If it's supposed to be altplus or alt+z then you should use that information or a text file that a
by
Peter Molfese
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AFNI Message Board
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