Show all posts by user
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
I believe that afni_proc.py uses 3dToutcount
3dToutcount documentation
by
Peter Molfese
-
AFNI Message Board
Marcio,
Have you tried the no.glib version?
http://afni.nimh.nih.gov/pub/dist/tgz/macosx_10.6_Intel_64.no.glib.tgz
by
Peter Molfese
-
AFNI Message Board
You could use this type of approach:
Or use 3dcalc in a similar way to having multiple ROIs on the same map. Threshold the images for significance where anything significant is set to 1 in each overlay. Then do something along the lines of:
3dcalc -a firstOverlay+tlrc -b secondOverlay+tlrc -c thirdOverlay+tlrc -prefix combined -expr '1*a + 2*b + 3*c'
Then you can have th
by
Peter Molfese
-
AFNI Message Board
I had a similar problem with older binaries. What build are you running of afni (afni -version)? And what are you using to convert DICOM to NIFTI?
by
Peter Molfese
-
AFNI Message Board
This may not be a perfect answer to your question, but have you checked out slow_surf_clustsim.py included in the AFNI binaries?
by
Peter Molfese
-
AFNI Message Board
You can use 3dRegAna or 3dttest++.
If you use 3dRegAna, you can run a simple regression with one predictor, then take the square root of the R^2 term and take the sign of the b-value coefficient.
With 3dttest++, you can use the covariate file.
by
Peter Molfese
-
AFNI Message Board
This may be an "old school" approach, but here goes... Since you have warped to tlrc in your pipeline you can use the TT_N27+tlrc template (the default for afni_proc.py) to construct a mask.
1. Copy the file from your afni folder:
3dcopy ~/abin/TT_N27+tlrc ~/Desktop/your_files/TT_N27+tlrc
2. Create a mask from that template:
3dAutomask -prefix TT_Mask TT_N27+tlrc
3. Modify
by
Peter Molfese
-
AFNI Message Board
I've had a few problems with MATLAB resetting the library path. As a fix, I've appending the following to all AFNI commands before calling them via MATLAB. Hope this helps!
export DYLD_LIBRARY_PATH=""
So for example a command to do quick masking of a dataset via 3dcalc looks like this:
mask_command = ['export DYLD_LIBRARY_PATH=""; 3dcalc -a
by
Peter Molfese
-
AFNI Message Board
Very much looking forward to trying these programs out in the next couple of weeks!
by
Peter Molfese
-
AFNI Message Board
That 12-core Mac should be great for processing! Assuming you have about 3GB of RAM per processor, you can use the Mac as both an Xgrid Controller and Client to batch process all of the freesurfer jobs. See this post on the Freesurfer wiki:
by
Peter Molfese
-
AFNI Message Board
After deciding on a cutoff for an outlier volume, you can use 1deval to determine if it's over threshold and write a 1D file for each run (1's are keep that TR, 0's are censor them). Concatenate those files (e.g. cat). Then put them into 3dDeconvolve using the "-censor" flag.
If you wanted to use afni_proc.py with dmBLOCK, you can use sed to do a quick replacement
by
Peter Molfese
-
AFNI Message Board