Difference between revisions of "Neuroimaging"
From ACL@NCU
| Line 4: | Line 4: | ||
== Preprocessing == | == Preprocessing == | ||
#Data import | #Data import | ||
* | *use to3d or dimon to convert raw images into AFNI BRIK format | ||
* | *to3d_anat.py, to3d_func.py | ||
*Data file organizations | |||
#creating group list | |||
## getid.py | |||
# | #looking for the sequential order ID one or more subjects | ||
##lookup_subj.py | |||
##lookup_subj_many.py | |||
== Individual level GLM == | == Individual level GLM == | ||
Revision as of 06:44, 18 January 2013
AFNI know-how
Preprocessing
- Data import
- use to3d or dimon to convert raw images into AFNI BRIK format
- to3d_anat.py, to3d_func.py
- Data file organizations
- creating group list
- getid.py
- looking for the sequential order ID one or more subjects
- lookup_subj.py
- lookup_subj_many.py
Individual level GLM
Group analysis
Multiple comparison
Region-of-Interest (ROI)
- Creating a half hemisphere mask
#left hemisphere selected
3dcalc -a mask_group+tlrc. -expr 'step(x-0)' -prefix test
#intersection with brain mask, and save in rh_mask+tlrc
3dcalc -a mask_group+tlrc. -b test+tlrc -expr 'step(a*b)' \
-prefix rh_mask
BrainVoyager QX know-how
Preprocessing
Individual level GLM
Group analysis
Multiple comparison
- Cluster threshold estimation (CTE)
- Forming valid mask[3]
- Masking and cluster thresholding[4]
- CTE in BVQX vs. other softwares (AFNI, SPM)[5]
- Solution to "Mask Not Valid!!" problem in CTE
Region-of-Interest (ROI)
FreeSurfurer tutorials
- view data
tkmedit sub001 brain.finalsurfs.mgz -aux T1.mgz -surfs -aseg
- syntax
- sub001: Subject ID
- brain.finalsurfs.mgz: skull-stripped volume primarily used for troubleshooting (found in $SUBJECTS_DIR/good_output/mri).
- aux T1.mgz : pre-skull-stripped volume loaded as 2nd volume (in $SUBJECTS_DIR/good_output/mri)
- surfs : loads all surfaces (orig, white, and pial, for left and right hemispheres)
- aseg : loads automatic volume segmentation called aseg.mgz