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
Page 1 of 1 Pages: 1
Results 1 - 7 of 7
I re-ran with -giant_move in the align_opts and it's worse. see attached.
by
mamlung-KU
-
AFNI Message Board
Hi Rick,
Attached image of the ve2a block. Looks like alignment failed there, too.
Did not include -giant_move, but align_unifize_epi local is included
Here's the command:
afni_proc.py \
-subj_id $name \
-copy_anat $name.T1+orig \
-anat_has_skull yes \
-dsets $name.apt1+orig $name.apt2+orig $name.apt3+orig $name.apt4+orig \
-blocks tshift align tlrc volreg blur mask sca
by
mamlung-KU
-
AFNI Message Board
Last login: Mon Nov 21 19:02:29 on ttys000
-------- freesurfer-Darwin-lion-stable-pub-v5.3.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/subjects
MNI_DIR /Applications/freesurfer/mni
FSL_DIR
by
mamlung-KU
-
AFNI Message Board
I'm reviewing the QC for one of our participants and the alignment is not very good at all. I'm not sure why, so I was hoping you could give me some ideas about what might be happening here.
Our old piecemeal pipeline (did not have an alignment step, just VR and TLRC) yielded much better correspondence between the anatomical and output of 3dDeconvolve. The first attachment shows the
by
mamlung-KU
-
AFNI Message Board
The QC output is outstanding and very helpful.
I'm trying to run Example 0 on the website you provided, but nothing is saving to my QC folder.
Here's my command:
set opref = QC/anat
@chauffeur_afni -ulay 2072_test.T1+orig -prefix ${opref} -set_xhairs MULTI -montx 3 -monty 3 -label_mode 1 -label_mode 4
The command seems to run fine (see terminal output below). But when
by
mamlung-KU
-
AFNI Message Board
Thank you for these very helpful suggestions!
While I'm talking with you, I was wondering if there is a way to generate activation montage images from the command line. We typically open our output in AFNI, open a montage view, set the overlay sub-brick, set the pval, and save a jpeg for each participant. I was wondering if theres a handy AFNI command or tool that would allow us to automa
by
mamlung-KU
-
AFNI Message Board
We are moving away from using our in-house analysis scripts to use afniproc.py. I was able to get the pipeline running successfully and am pleased with the results I am getting. We are considering two different analyses at the regress step. The difference is how trials are binned (either based on the task parameters or based on participant's behavioral responses, not really important to know
by
mamlung-KU
-
AFNI Message Board