Neuroimaging

AFNI know-how

Preprocessing

1. Data import
   1. use to3d or dimon to convert raw images into AFNI BRIK format
   2. to3d_anat.py, to3d_func.py
   3. Data file organizations
1. creating group list
   1. getid.py
2. looking for the sequential order ID one or more subjects
   1. lookup_subj.py
   2. lookup_subj_many.py

1. Deoblique

• N.B.: EPI time series data should be time shifted with 3dTshift before rotating the volumes to a cardinal direction

3dWarp -deoblique

Group analysis[1]

• Average group T1

Copy 3D+tlrc.BRIK & .HEAD into your "average" directory

3dmerge -doall 3d*+tlrc* 

(where "3d*+tlrc* is using enough wild cards to get all the 3D anatomy files you want to average)

The output name is mrg+tlrc.BRIK and mrg+tlrc.HEAD by default, but you can use the -prefix flag to specify an output prefix (other than mrg) that you prefer.

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

• Convert a multi-cluster mask to a union mask (each ROI with the same value)

3dcalc -a Clust_N_Control_p005_mask+tlrc -expr 'notzero(a)' -prefix Clust_N_Control_p005_maskp

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Misc.

• Converting a single t-value to z-value

ccalc -expr 'fitt_t2z(t, n)' 
t: tvalue
n: degrees of freedom

• Converting t-value sub-brick to z-value sub-brick

3dcalc -a dset+tlrc[<t-map_id>] \
  -expr 'fitt_t2z(3, 10)' -prefix dset2 

• listing all subbriks in a BRIK file and add numerical index

3dinfo -label <BRIK filename> | sed 's/|/\n/g' | nl

• Segmentation (not recommended for quantitative use)

3dSeg 	-anat <anatfile> -mask AUTO \
	-classes 'CSF ; GM ; WM' -bias_classes 'GM ; WM' \
      	-bias_fwhm 25 -mixfrac UNI -main_N 5 \
      	-blur_meth BFT -prefix <output file>

• Extracting grey matter mask from segmented brain

3dcalc -a Classes+tlrc'<GM>' -expr 'step(a)' -prefix TT_icbm452_GMseg

• resample the mask to a coarse resolution

3dresample -dxyz 3 3 3 -rmode 'Cu' -inset TT_icbm452_GMseg+tlrc -prefix TT_icbm_GMseg3mm 

• Create partial union mask for a group of anatomical masks

#partial union mask
3dmask_tool -frac 0.3 -input *_GMseg+tlrc.HEAD -prefix punion_0.3.mask

• Look-up dicom raw data header (ID creation time in this case)

dicom_hdr <filename> | grep 'ID Instance Creation Time'

BrainVoyager QX know-how

Group analysis

• Created individual vmps[2]
• Paired t-test on vmps[3]

Multiple comparison

• Cluster threshold estimation (CTE)
  • Forming valid mask[4]
  • Masking and cluster thresholding[5]
  • CTE in BVQX vs. other softwares (AFNI, SPM)[6]
  • Solution to "Mask Not Valid!!" problem in CTE

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