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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
Job Announcement: Associate Director of MRI Operations
The University of Connecticut invites applications for the position of Associate Director of MRI Operations. This full-time, renewable, 11-month, non tenure-track appointment is for an assistant research professor. UConn’s Brain Imaging Research Center is a 3200 square foot research facility housing a Siemens Prisma 3 Tesla scanner. Th
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Peter Molfese
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AFNI Message Board
Bash syntax for people who like it:
export DYLD_LIBRARY_PATH=/opt/X11/lib/flat_namespace
or if you wish to just add it to the relevant files on a Mac:
echo "export DYLD_LIBRARY_PATH=/opt/X11/lib/flat_namespace" >> .bash_profile
or most variants of Linux:
echo "export DYLD_LIBRARY_PATH=/opt/X11/lib/flat_namespace" >> .bashrc
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Peter Molfese
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AFNI Message Board
Hi Shana-
It's usually a good idea to do your preprocessing in afni_proc.py or uber_subject. This ensures that the projecting of the data to the surfaces happens in a fairly accurate way (before smoothing) and also allows you to smooth on the cortical surface! There can be some sizable differences when you do the surface smoothing compared to the more "traditional" in volume s
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Peter Molfese
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AFNI Message Board
Hi Shana-
The correct (read: most common, easiest, more tested) approach is:
1) Freesurfer on your original T1 anatomicals (with the skull on)
2) run @SUMA_Make_Spec_FS on the output folder
3) Use afni_proc.py (or uber_subject.py). See example 8. This will automatically perform the alignment between Freesurfer's anatomical, the surfaces, and the EPI. If you feed it the std.141 files
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Peter Molfese
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AFNI Message Board
Sometimes XQuartz needs a reboot before it works seamlessly with the terminal. Try that and post the output of:
afni_system_check.py -check_all
More info on that command here.
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Peter Molfese
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AFNI Message Board
Try adding the following to your script:
-align_opts_aea -giant_move
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Peter Molfese
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AFNI Message Board
Warnings are normal and expected. They are there to alert you that something may be going on. Notice that they'll go away after the align step is performed!
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Peter Molfese
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AFNI Message Board
I prefer to use the non-corrected series for data analysis for exactly the reason you point out. If you use the MOCO, it is not possible to include the exact motion parameters as regressors in your regression model.
Your script looks mostly standard. I usually only use the despike block in resting state analyses, and not in functional tasks.
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Peter Molfese
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AFNI Message Board
I prefer to use the non-corrected images for the reasons you ask. You cannot include exact motion regressors in your regression model if you use the MOCO. The fundamentals are mostly the same, but I prefer to trust in AFNI to do the heavy lifting. It's easier to see exactly what the software is doing!
Your script looks mostly standard based on the examples that are provided in afni_p
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Peter Molfese
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AFNI Message Board
It is not necessary if you have an align step in your script. Depending on the scanner parameters of each sequence, you may end up playing with options like "-giant_move".
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Peter Molfese
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AFNI Message Board
Interesting... Your install is pointing to a homebrew specific Ruby install.
Do you have Xcode installed on your system?
When you reinstalled, did you delete the /usr/local/Cellar folder and the /usr/local/bin folder?
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Peter Molfese
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AFNI Message Board
If it continues to hang, you can try removing all of homebrew (and probably everything in /usr/local) and then starting the installation instructions over again. Good luck! Upgrading is always an interesting process in terms of the UNIX side of things.
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Peter Molfese
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AFNI Message Board
That's really clever to use the t-stat Gang! Makes life considerably easier.
In my (now outdated) way of doing things, z-scoring the data would convert the b-value of the regression to a standardized regression coefficient (beta), which in simple regression is a correlation. So if you centered both of your datasets (MRI and covariates) the correlation value would appear in the "m
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Peter Molfese
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AFNI Message Board
You can use 3dttest++, but I personally prefer to use 3dTcorr1D.
My (fairly old) notes on using 3dttest++ or 3dMEMA is that you would need to standardize your MRI and behavioral measures beforehand.
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Peter Molfese
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AFNI Message Board
I usually suggest that people use the Freesurfer pipeline for the group analyses. However, if you want to use AFNI/SUMA, I wrote a blog post a while ago on one pipeline that has worked well for me, and produces results nearly identical to Freesurfer.
The advantage of the pipeline in that post is that it uses the Freesurfer pipeline for smoothing and getting all subjects onto the fsaverage (
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Peter Molfese
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AFNI Message Board
Hi Robin-
It is definitely hard to see all of the regions in the "Draw Dataset" plugin. I'll leave it to the AFNI guys to say if they can make a change to display the regions in a popup window.
I usually draw the atlas regions using the command line tool whereami. Using that tool, you can get a list of all of the atlases in AFNI using the following:
whereami -show_atla
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Peter Molfese
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AFNI Message Board
Usually you have to do 3dfractionize to match the resolution of the ROIs to your functional datasets. In my pipelines it is always a "must". A quick look at your two datasets will tell you if they match on resolution, something like this:
3dinfo -prefix -n4 -d3 ROIs+tlrc.HEAD stats+tlrc.HEAD
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Peter Molfese
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AFNI Message Board
Hi Emily,
Dimon really likes each run to be separated into separate folders. Fortunate, there's a script for that - @move.to.series.dirs. On data I have from Martinos it has worked quite well. You can then run Dimon to later convert each series on each resulting folder separately.
Best,
Peter
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Peter Molfese
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AFNI Message Board
These warnings are normal, and not cause for concern!
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Peter Molfese
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AFNI Message Board
What's the output of:
afni_system_check.py -check_all
Did you upgrade the Operating System at some point from 10.10 to 10.11?
Also, I'll be in your area tomorrow. I'll just stop by!
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Peter Molfese
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AFNI Message Board
It's always a long shot, but have you tried rebooting since reinstalling XQuartz?
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Peter Molfese
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AFNI Message Board
It looks like your structural image is also appearing in standard space (+tlrc). Again, if you are sure that it is in subject space, you can use 3drefit on the structurelle_sujet1.nii file just as you did before with the 4D.nii.
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Peter Molfese
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AFNI Message Board
Hello,
Can you post the entire output? Also, what's the output of 3dinfo on the structural scan (structurelle_sujet1.nii)?
-PM
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Peter Molfese
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AFNI Message Board
Hi Michele-
For whatever reason, AFNI believes your data are already in standard space. Has the data been preprocessed in any other software? How was it converted from DICOM?
If you are certain that the functional data is in subject space (+ORIG), then you can use 3drefit to adjust the parameters of the file and re-run your command.
Best,
Peter
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Peter Molfese
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AFNI Message Board
Hi Ajay-
I definitely don't have all of the answers to this one (at the moment). My understanding is that you do not have to provide a mask for surface datasets. Either vertices exist or they don't.
I find it a bit unusual that you're getting a value of 10mm on a surface file smoothed by Freesurfer to 15mm. In that past I've found that the smoothness tends to be a b
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Peter Molfese
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AFNI Message Board
I would use the input files to estimate the smoothness, as opposed to the output of 3dMVM. What smoothing factor did you use coming out of Freesurfer?
PM
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Peter Molfese
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AFNI Message Board
Hi Ajay,
I haven't checked how Qdec does things in a while. But it could be that you need to dummy code the categorical variables to get the same results. I have vague memories of creating factor variables in Freesurfer that are treated differently by mri_glmfit, but again it's been a while. Also, I don't think that Freesurfer will automatically center the variables for you.
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Peter Molfese
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AFNI Message Board
Typically we specify multi-slice files using the custom @filename. So put your onset times into a text (or 1D) file and then point 3dTshift to that file using its absolute path.
There are some who don't bother to slice time correct multi-slice data. Worth taking note of the sequence you are using (typically the CMRR, MGH, Siemens WIP) and seeing what others are doing with your acceler
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Peter Molfese
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AFNI Message Board