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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
Hi Peng,
Oh good, just checking. I was feeling a bit decaffeinated this morning and didn't dig into it originally. You lose one degree of freedom for the intercept and one for your covariate. Yes, the DF is consistent across voxels. You could allow DFs to vary across voxels with options in 3dttest++, but then my ability to guide you in the process of interpreting the results requires
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Peter Molfese
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AFNI Message Board
The output says you have 6 degrees of freedom (statpar = 6). I'm curious what is in your covariates.1D file, and if it includes the intercept, which would be unnecessary, and be eating one of your DFs.
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Peter Molfese
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AFNI Message Board
3dinfo should give you the DF for the t-test in the results.
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Peter Molfese
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AFNI Message Board
Hi Peng,
You can follow this blog post for some guidance on how to do brain behavior correlation.
You're running a 1-sample t-test with covariate file and then converting the t-stat to an R-squared and taking the square root.
-Peter
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Peter Molfese
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AFNI Message Board
The screenshot looks like you're showing the direct DICOM converted datasets. It's rare that I'd expect to see those in perfect alignment just due to the sheer number of ways of interpreting coordinates from a DICOM file. The image that you might want to look at are the pb03 or pb04 within the results folder which should include the align step. If you're still not seeing go
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Peter Molfese
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AFNI Message Board
Feel free to post your entire command in a code box. But likely caused by not having a backslash continuation at the end of each filename. In linux/unix a "\" will tell the shell to continue to the next line and keep reading inputs. So each line in the command should end with that except the last one.
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Peter Molfese
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AFNI Message Board
You can disable gatekeeper entirely.
Run the following command in your terminal: sudo spctl --master-disable
In System Preferences > Security & Privacy > "Allow apps from" > Anywhere.
That should get you the rest of the way. I suppose we could figure out how to sign AFNI apps, but I suspect the communities will offer other workarounds as the install base of 10
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Peter Molfese
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AFNI Message Board
You need to relax the GateKeeper settings. You can read about it here.
Searching towards the bottom is: "How to open an app that hasn’t been notarized or is from an unidentified developer".
Generally it takes us a little bit of time to verify everything on a new OS. For production scientific computers, I would recommend waiting some time before upgrading to a new OS release.
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Peter Molfese
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AFNI Message Board
If it's a GIFTI/Surface you can use ConvertSurface, which supports PLY and STL (among others). For volumes, it gets more complex, and usually easiest to convert it to a Surface (IsoSurface) and then use ConvertSurface.
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Peter Molfese
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AFNI Message Board
You can do the pairwise correlations with 3dTcorrelate and then Gang is finishing up work on 3dISC, the group level analysis program, but he may be willing to send you a less pretty script that will do the LME part of things.
There's also the BrainIAK project which has group analysis ISC methods. It's fairly easy to do this from the pairwise steps from AFNI as well.
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Peter Molfese
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AFNI Message Board
You can get a list from 3dAttribute or 3dinfo. If you wanted to split it apart, you can use 3dTsplit4D.
Another route would be to use 3dROIstats which conveniently has a new "-longnames" option, and that'll give you the names of each sub-brik in a set.
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Peter Molfese
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AFNI Message Board
The entire header? You could use nifti_tool to write fields and loop through that way... A more efficient route might be to use nibabel or try to modify the reconstructed DICOM files using pydicom.
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Peter Molfese
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AFNI Message Board
Assuming you've already run @SUMA_Make_Spec_FS along with the MapIcosahedron step, you can use SurfToSurf. There's an example in the MapIcosahedron help file at the end.
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Peter Molfese
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AFNI Message Board
Yes.
The first step is to convert the label into an annotation in Freesurfer using mris_label2annot. Once you have that, you can use FSread_annot to convert it to SUMA. You may need to also run ROI2dataset depending on what you want to do. And then SurfToSurf with padding should take it the final step.
-Peter
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Peter Molfese
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AFNI Message Board
Greetings 2086,
Do you already have the labels in an AFNI related format (niml.dset or gii)? You can use SurfToSurf to go from one surface space to another (e.g. FS Average to subject or back again). You can also transform that fsaverage space label to the standard label (std.141.*) and then map it to any surface.
-Peter
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Peter Molfese
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AFNI Message Board
Hi Paul,
You can change the -master to be the same as the input, that should avoid the system trying to add slices/interpolate.
-PM
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Peter Molfese
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AFNI Message Board
Hi Paul-
I think much of the problem is caused by how you Z-padded the image. It looks like you were taking out slices instead of adding. My final commands to get pretty decent alignment are below. I did skull strip both anatomicals.
#strip anatomical
3dSkullStrip -input anat.nii -prefix anat_ns.nii
#z-pad low-res image
3dZeropad -I 20 -P 20 -A 20 -S 20 -L 20 -R 20 -prefix T1_ZP.n
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Peter Molfese
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AFNI Message Board
Hmm, looks like you're using a newer Python. What's the output of:
afni_system_check.py -check_all
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Peter Molfese
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AFNI Message Board
Try specifying the full path to the slicetimes.1D file.
You can try to use -copy_files inside the afni_proc.py script setup to copy the necessary slicetimes file like the anatomical is copied. My memory is that this also works.
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Peter Molfese
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AFNI Message Board
Hi Paul-
It should work for any partial coverage situation. If you have specific data you'd like us to demo with, I'm happy to do that.
-Peter
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Peter Molfese
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AFNI Message Board
Good to know. In addition to regularly updating... a good:
suma -update_env
Can go a long way.
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Peter Molfese
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AFNI Message Board
Since your last data didn't require any nudging, can you upload the current troublesome data?
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Peter Molfese
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AFNI Message Board
Ruyuan-
We're working on tools that are more high-field specific. Generally I use 3drefit to move the slab into an approximate position and orientation. Zeropad the functional data, and then use 3dAllineate to work the actual alignment. As I said before, DO NOT use align_epi_anat.py until we have a chance to better modify the options to deal with partial data. You're welcome to u
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Peter Molfese
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AFNI Message Board
That's definitely a Paul. Though if he says no, I'm sure you could persuade me to do it.
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Peter Molfese
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AFNI Message Board
I think we need to make some modifications to align_epi_anat.py's functions regarding partial-coverage. So for now, I would recommend using 3dAllineate directly with the options specified.
For the nudge, I would go ahead and use the plugin, followed by 3dAllineate to do a quick alignment to get a rigid alignment (-warp shirt_rotate), and use cat_matvec to concatenate your two transform
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Peter Molfese
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AFNI Message Board
I'll also add that if you wanted to, you could build any version of AFNI using the github pull and an updated Makefile that I wrote specifically for 10.14 (probably 10.13 too) that uses homebrew for dependencies and Anaconda for Python. It's part of the distribution and a solid starting point. Let me know if you have questions should you decide to build other iterations.
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Peter Molfese
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AFNI Message Board
Hi Ruyuan-
PTaylor and I got it working after a few tries. The major thing is to Zeropad your input. Basic flow of our test was to skullstrip your anatomical, zero pad the EPI and then align using 3dAllineate.
@SSwarper -input C1051_SurfVol.nii.gz -base MNI152_2009_template_SSW.nii.gz -subid Subj01 -skipwarp
3dZeropad -I 20 -P 20 -A 5 -prefix epi1_rs.nii.gz epi_mean_test.nii.gz
#
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Peter Molfese
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AFNI Message Board