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Difference between revisions of "Neuroimaging"

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#partial union mask
#partial union mask
3dmask_tool -frac 0.3 -input *_GMseg+tlrc.HEAD -prefix punion_0.3.mask
3dmask_tool -frac 0.3 -input *_GMseg+tlrc.HEAD -prefix punion_0.3.mask
</pre>
*Look-up dicom raw data header (ID creation time in this case)
<pre>
dicom_hdr <filename> | grep 'ID Instance Creation Time'
</pre>
</pre>



Revision as of 08:45, 26 April 2013

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

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
  • 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

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

Preprocessing

Individual level GLM

Group analysis

  • Created individual vmps[1]
  • Paired t-test on vmps[2]

Multiple comparison

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